Compounds and methods for diagnosis and treatment of leishmaniasis

ABSTRACT

Compounds and methods are provided for diagnosing, preventing, treating and detecting leishmaniasis infection and stimulating immune responses in patients are disclosed. The compounds disclosed are include polypeptides and fusion proteins that contain at least one immunogenic portion of one or more  Leishmania  antigens, or a variant thereof. Additionally, methods of screening a screening library for tandem repeat proteins that have immunogenic properties are disclosed. Vaccines and pharmaceutical compositions comprising polynucleotides, polypeptides, fusion proteins and variants thereof that may be used for the prevention and therapy of leishmaniasis, as well as for the detection of Leishmaniasis infection are described.

PRIORITY CLAIM

This application claims priority to U.S. Provisional Application60/791,226 filed Apr. 10, 2006. The foregoing application is herebyincorporated by reference in its entirety as if fully set forth herein.

This application claims priority to U.S. Provisional Application60/744,798 filed Apr. 13, 2006. The foregoing application is herebyincorporated by reference in its entirety as if fully set forth herein.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made in part with government support under Grant No.AI-25038 awarded by the National Institutes of Health. The governmenthas certain rights in this invention.

FIELD OF THE INVENTION

The present invention relates generally to the serodiagnosis ofLeishmania infection. The invention is more particularly directed to theuse of one or more Leishmania polypeptides in methods and diagnostickits to screen organisms and blood supplies for Leishmania, and toidentify those individuals that are likely to progress to acute visceralleishmaniasis. The invention is also directed to vaccines andpharmaceutical compositions for treating and immunizing an organismagainst leishmaniasis.

BACKGROUND OF THE INVENTION

Leishmania organisms are intracellular protozoan parasites ofmacrophages that cause a wide range of clinical diseases in humans anddomestic animals, primarily dogs. In some infections, the parasite maylie dormant for many years. In other cases, the host may develop one ofa variety of forms of leishmaniasis. For example, the disease may beasymptomatic or may be manifested as sub-clinical visceralleishmaniasis, which is characterized by mild symptoms of malaise,diarrhea and intermittent hepatomegaly. Patients with sub-clinical orasymptomatic disease usually have low antibody titers, making thedisease difficult to detect with standard techniques. Alternatively,leishmaniasis may be manifested as a cutaneous disease, which is asevere medical problem but is generally self-limiting, or as a highlydestructive mucosal disease, which is not self-limiting. Finally, andmost seriously, the disease may be manifested as an acute visceralinfection involving the spleen, liver and lymph nodes, which, untreated,is generally a fatal disease. Symptoms of acute visceral leishmaniasisinclude hepatosplenomegaly, fever, leukopenia, anemia andhypergammaglobulinemia.

Leishmaniasis is a serious problem in much of the world, includingBrazil, China, East Africa, India and areas of the Middle East. Thedisease is also endemic in the Mediterranean region, including southernFrance, Italy, Greece, Spain, Portugal and North Africa. The number ofcases of leishmaniasis has increased dramatically in the last 20 years,and millions of cases of this disease now exist worldwide. About 2million new cases are diagnosed each year, 25% of which are visceralleishmaniasis. There are, however, no vaccines or effective treatmentscurrently available.

Diagnosis of Visceral leishmaniasis can not always be made only on thebasis of clinical symptoms because visceral leishmaniasis shares itsclinical features with other diseases such as malaria, typhoid fever andtuberculosis occurring commonly in the same endemic areas. Thus, thediagnosis of visceral leishmaniasis largely relies on parasitological orserological methods. The former is microscopic detection of amastigotesin aspirates of spleen and bone marrow or detection of promastigotesthrough cultivation of the aspirates. Unfortunately, this methodrequires the biopsy of bone marrow, liver, spleen, or lymph nodes may berequired, which may lead to secondary infection or further disfigurementof the patient. Additionally, along with being an invasive diagnosis, ittakes a long period of time to diagnose and results are commonlynon-conclusive. Therefore, this method is invasive, time-consuming, andnot sufficiently sensitive, thereby rendering it inefficient.

Less invasive and time consuming laboratory procedures do exist,however, these procedures suffer from either lack of sensitivity orcumbersome implementation. For example the Liquid Direct AgglutinationTest (LQ DAT: Ahfad University, Khartoum and IPB, Addis Abbeba) and theFreeze Dried DAT (FD DAT: Meredith et al. 1995) have good sensitivity,but require multiple pipetting steps and incubation, which makesimplementation of this test difficult in developing countries.Similarly, the Latex Antigen Agglutination Test in Urine (KATEX®: KalonBiological Ltd-UK) has good sensitivity and specificity, but requires acumbersome urine boiling step and further suffers from lowreproducibility. Finally, the rK39 and rK26 dipstick tests (Inbios®,Seattle, Wash.) can rapidly give results within a matter of minutes, butthese tests lack sensitivity in certain geographic regions such asSudan, Ethiopia and Kenya. Because the dipstick tests can be easily,quickly, and affordably implemented, yet suffer from lack of antigensensitivity, discovery of new antigens is necessary for more accuratediagnosis of leishmaniasis.

Among defined leishmanial antigens reported previously, rK39 appears tobe the best antigen for serodiagnosis of visceral leishmaniasis in termsof both sensitivity and specificity. rK39 is sensitive and reliable evenon a strip format, which is feasible for field use, and the rK39 striptest has high sensitivity in India, Nepal and Brazil. In Sudan, Ethiopiaand Kenya, however, the sensitivity of the strip test falls to 67% andthe negative responses on the strip test appear to correlate with lowerreactivity by ELISA. Thus, new diagnostic antigens are needed tocomplement rK39 to contribute to the development of a more accuratediagnosis of leishmaniasis. The present invention fulfills these needsand many other related needs.

SUMMARY OF THE INVENTION

Briefly stated, this invention relates to compounds and methods fordetecting and treating leishmaniasis in individuals and in bloodsupplies.

More specifically, compounds and methods are provided for diagnosing,preventing, treating and detecting leishmaniasis infection andstimulating immune responses in patients are disclosed. The compoundsdisclosed include polypeptides and fusion proteins that contain at leastone immunogenic portion of one or more Leishmania antigens, or a variantthereof. Additionally, methods of screening a screening library fortandem repeat proteins that have immunogenic properties are disclosed.Vaccines and pharmaceutical compositions comprising polynucleotides,polypeptides, fusion proteins and variants thereof that may be used forthe prevention and therapy of leishmaniasis, as well as for thedetection of Leishmaniasis infection are described.

In one embodiment a method for detecting Leishmania infection isdisclosed that comprises the steps of first contacting a biologicalsample with polypeptides comprising at least one tandem repeat unit,wherein the tandem repeat unit comprises an amino acid sequence havinghomology to, an amino acid sequence selected from the group consistingof SEQ ID NO: 1-59; and second detecting the presence of antibodies inthe biological sample to detect Leishmaniasis infection. Relatedembodiments include similar methods of using tandem repeat proteins andfusion proteins that comprise one or more of the amino acid sequences ofSEQ ID NO: 1-59. In still further embodiments, diagnostic kits fordetecting Leishmania infection are disclosed that comprise thepolypeptides described above.

In still further embodiments of the present invention, DNA sequencesencoding the polypeptides described above are disclosed in addition toexpression vectors and host cells comprising the same.

Additional embodiments are disclosed wherein the polypeptides disclosedare used in pharmacological compositions and related methods of usingthese pharmacological compositions to treat, detect, and immunizingagainst Leishmania infection are disclosed.

In other embodiments, methods for screening for immunogenic polypeptidesare disclosed, which comprise the steps of constructing a screeninglibrary, screening the library with a biological sample and analyzingidentified sequences to select for tandem repeat genes. Still furthermethods are disclosed for embodiments of the present invention where oneor more polypeptide or polynucleotide sequences are selected and thenscreened for tandem repeat domains so as to screen for immunogenicpolynucleotides or immunogenic polypeptides.

BRIEF DESCRIPTION OF THE DRAWINGS

Preferred and alternate embodiments of the present invention aredescribed in detail below with reference to the following drawings:

FIG. 1 shows a representative PCR analysis of tandem repeat genes. PCRreactions performed with primer sets specific for the tandem repeatregions of LinJ16.1750, LinJ22.1590 and LinJ33.2870 or for a T. cruzigene using total DNA of L. infantum (Li), L. donovani (Ld), L. major(Lm), L. amazonensis (La) and T. cruzi (Tc) as templates. Sizes areshown in base pairs.

FIG. 2 illustrates an exemplary expression and purification of L.infantum recombinant proteins. Shown are coomassie blue-stainedSDS/4-20% polyacrylamide gradient gels of uninduced E. coli lysates(lane 1), induced lysates (lane 2) and purified proteins (lane 3). Sizesare shown in kDa.

FIG. 3 presents a demonstrative enzyme-linked immunosorbent assayevaluation of patient seroreactivity to L. infantum recombinantproteins. Patient sera from patients of visceral leishmaniasis (VL,n=10), cutaneous leishmaniasis (CL, n=10), tuberculosis (TB, n=10),malaria (n=6), or sera from healthy controls in United States (n=10)were used. Mean and SEM of OD values in each group are shown.

FIG. 4 shows representative reactivity of human visceral leishmaniasispatient sera to tandem repeat proteins. Sera from visceral leishmaniasispatients (n=35) and healthy controls (n=20) were tested for reactivityto rLinJ16.1750r2 or rK39 by ELISA. Mean in each group is shown as asolid line. Dotted lines represent cutoff values calculated as mean+3SDof OD values from healthy controls.

FIG. 5 illustrates exemplary recognition of recombinant proteins by serafrom eight visceral leishmaniasis patients, which showed low reactivityto rK39 (OD<1.0, circled in FIG. 4).

FIG. 6 shows demonstrative antibody responses of visceral leishmaniasispatient sera to tandem repeat proteins. Sera from visceral leishmaniasispatients (closed circles: n=16) and healthy controls (open circles: n=8)were tested for their reactivity to tandem repeat proteins by ELISA andOD values of each individuals are shown. Bars represent means of eachgroup.

DETAILED DESCRIPTION

As stated above the present invention relates to compositions andmethods for detecting and protecting against Leishmania infection in abiological sample or organism, in addition to methods for screening andidentifying compounds that have efficacy in detecting and protectingagainst Leishmania infection in a biological sample or organism.

In one embodiment, the invention provides a method compounds fordetecting Leishmania infection in a biological sample or organism,comprising: (a) contacting a biological sample with one or morepolypeptides at least one of which comprises one or more tandem repeatunits or a variant thereof that only differs in conservativesubstitutions or modifications, which tandem repeat unit in certainembodiments comprises an amino acid sequence having at least 8consecutive amino acids of, and at least 70% sequence homology to, anamino acid sequence selected from SEQ ID NOS:1-59, under conditions andfor a time sufficient for binding to the polypeptide(s) by an antibodyin the sample to take place; and (b) detecting in the biological samplethe presence of one or a plurality of antibodies that specifically bindto the polypeptide, thereby detecting Leishmania infection in thebiological sample.

In another embodiment, the invention provides methods and compositionsfor detecting Leishmania infection in a biological sample or organism,comprising: (a) contacting a biological sample with a compositioncomprising a polypeptide that comprises a tandem repeat unit, or avariant thereof that only differs in conservative substitutions ormodifications under conditions and for a time sufficient for binding tothe polypeptide(s) by an antibody in the sample to take place; and (b)detecting in the biological sample the presence of antibodies that bindto the polypeptide, thereby detecting Leishmania infection in thebiological sample. In these and other related embodiments thecomposition may include a single tandem repeat as provided herein, ormay include two or more tandem repeat units which may be the same ordifferent. This composition may thus comprise one or more species oftandem repeat unit, and/or may also include fusion proteins comprisingone or more species of tandem repeat unit.

In a still further embodiment, the invention provides methods forscreening and selecting tandem repeat proteins that have efficacy indetecting Leishmania infection in a biological sample or organismcomprising: (a) constructing a Leishmania screening library; (b)screening the Leishmania screening library; and (c) analyzing the genesidentified from the screening the Leishmania screening library to selectgenes that are tandem repeat genes.

In yet another embodiment, the invention provides systems and methodsfor treating and detecting leishmaniasis in patients with clinical orsub-clinical leishmaniasis infection.

Polypeptides that are contemplated according to certain embodiments ofthe present invention include, but are not limited to, polypeptidescomprising immunogenic portions of Leishmania antigens comprising thesequences recited in SEQ ID NO:1-59. As used herein, the term“polypeptide” encompasses amino acid chains of any length, includingfull length proteins (i.e., antigens), wherein the amino acid residuesare covalently linked as linear polymers by peptide bonds. Thus, apolypeptide comprising an immunogenic portion of one of the aboveantigens may consist entirely of the immunogenic portion, or may containadditional sequences. The additional sequences may be naturallyoccurring sequences such as sequences derived from the native Leishmaniaantigen, or may be heterologous (e.g., derived from other sourcesincluding exogenous naturally occurring sequences and/or artificialsequences), and such sequences may (but need not) be immunogenic. Anantigen “having” a particular recited sequence is an antigen thatcomprises a recited sequence, e.g., that contains, within its fulllength sequence, the recited sequence. The native antigen may, or maynot, contain one or more additional amino acid sequences. A material,molecule, preparation or the like which is “isolated” refers to itshaving been removed from the environment or source in which it naturallyoccurs. For example, a polynucleotide sequence which is part of a genepresent on a chromosome in a subject or biological source such as anintact, living animal is not isolated, while DNA extracted from abiological sample that has been obtained from such a subject orbiological source would be considered isolated. In like fashion,“isolating” may refer to steps taken in the processes or methods forremoving such a material from the natural environment in which itoccurs.

As used herein, the term “tandem repeat” refers to a region of apolynucleotide sequence (e.g., a sequence of DNA, RNA, recombinantlyengineered or synthetic oligonucleotides including linear polymers ofnon-naturally occurring nucleotides or nucleotide analogs or the like,including nucleotide mimetics) or to a region of a polypeptide orprotein comprising a sequence, respectively, of about 6 to 1200nucleotides or 2 to 400 amino acids, that is repeated in tandem suchthat the sequence occurs at least two times. As used herein the term“tandem repeat unit” refers to a single unit of the sequence that isrepeated in tandem. Additionally, the term “tandem repeat” alsoencompasses a region of DNA wherein more than a single 2- to 400-aminoacid or 6- to 1200-nucleotide tandem repeat unit is repeated in tandemor with intervening bases or amino acids, provided that at least one ofthe sequences is repeated at least two times in tandem. Moreover, theterm “tandem repeat” also encompasses regions of DNA or a proteinwherein the tandem repeat units are not identical. Where two or moresequences are at least 70% homologous to each other or are reasonablevariants of each other, these sequences will be considered tandem repeatunits for the purpose of comprising and constituting a tandem repeat.

Also, where a sequence is at least 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22 or more amino acids of a tandem repeat unit,this sequence will be considered a tandem repeat unit for the purpose ofcomprising and constituting a tandem repeat.

Also, where a sequence is at least about 18, 21, 24, 27, 30, 33, 36, 39,42, 45, 48, 51 or any intervening integer of nucleotides, the sequencewill be considered a tandem repeat unit for the purpose of comprisingand constituting a tandem repeat.

Additionally, the term “tandem repeat” also encompasses tandem repeatswhere one or more tandem repeat unit of a tandem repeat is the reversesequence of the other tandem repeat units. Reverse tandem repeat unitsand non-reverse tandem repeats can be configured in any way and with orwithout intervening nucleotide bases or amino acids. Configurations ofreverse and non-reverse sequences include, but are not limited to, thosewhere a non-reverse sequence is followed by reverse sequence; where areverse sequence is followed by non-reverse sequence; and where areverse sequence is followed by a reverse sequence. In the case ofdouble-stranded polynucleotides having tandem repeats two or more suchrepeats may be present on the same strand or may occur on oppositestrands.

In certain preferred embodiments a tandem repeat may comprise animmunogenic portion of a Leishmania antigen. An immunogenic portion of aLeishmania antigen is a portion that is capable of eliciting an immuneresponse (i.e., cellular and/or humoral) in a presently or previouslyLeishmania-infected patient (such as a human or a dog) and/or incultures of lymph node cells or peripheral blood mononuclear cells(PBMC) isolated from presently or previously Leishmania-infectedindividuals. Those skilled in the art will be familiar with any of awide variety of methodologies and criteria for determining whether animmune response has been elicited. (See, e.g., Current Protocols inImmunology, John Wiley & Sons Publishers, NY 2000, Chapter 2, Units2.1-2.3) The cells in which a response is elicited may comprise amixture of cell types or may contain isolated component cells(including, but not limited to, T-cells, NK cells, macrophages,monocytes and/or B cells). In particular, immunogenic portions arecapable of inducing T-cell proliferation and/or a dominantly Th1-typecytokine response (e.g., IL-2, IFN-.gamma., and/or TNF-.alpha.production by T-cells and/or NK cells; and/or IL-12 production bymonocytes, macrophages and/or B cells). Immunogenic portions of theantigens described herein may generally be identified using techniquesknown to those of ordinary skill in the art, including therepresentative methods provided herein.

The compositions and methods of the present invention also encompassvariants of the above polypeptides. A polypeptide “variant,” or apolypeptide that is “homologous” to another protein as used herein, is apolypeptide that differs from a native (e.g., naturally occurring)protein in one or more substitutions, deletions, additions and/orinsertions, such that the immunogenicity of the polypeptide is notsubstantially diminished. For instance, the ability of a variant toreact with an antigen-specific antibody, antiserum or T cell may beenhanced or unchanged, relative to the native protein, or may bediminished by less than 50%, and preferably less than 20%, relative tothe native protein. Such variants may generally be identified bymodifying one of the herein described polypeptide sequences andevaluating the reactivity of the modified polypeptide withantigen-specific antibodies or antisera as described herein. Preferredvariants include those in which one or more portions, such as anN-terminal leader sequence or transmembrane domain, have been removed.Other preferred variants include variants in which a small portion(e.g., 1-30 amino acids, preferably 5-15 amino acids) has been removedfrom the N- and/or C-terminal of the mature protein.

Polypeptide variants encompassed by the present invention include thoseexhibiting at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99% or more identity (determined as described below)to the polypeptides disclosed herein.

Preferably, a variant contains conservative substitutions. A“conservative substitution” is one in which an amino acid is substitutedfor another amino acid that has similar properties, such that oneskilled in the art of peptide chemistry would expect the secondarystructure and hydropathic nature of the polypeptide to be substantiallyunchanged. Amino acid substitutions may generally be made on the basisof similarity in polarity, charge, solubility, hydrophobicity,hydrophilicity and/or the amphipathic nature of the residues. Forexample, negatively charged amino acids include aspartic acid andglutamic acid; positively charged amino acids include lysine andarginine; and amino acids with uncharged polar head groups havingsimilar hydrophilicity values include leucine, isoleucine and valine;glycine and alanine; asparagine and glutamine; and serine, threonine,phenylalanine and tyrosine. Other groups of amino acids that mayrepresent conservative changes include: (1) ala, pro, gly, glu, asp,gln, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala,phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. A variant may also,or alternatively, contain nonconservative changes. In a preferredembodiment, variant polypeptides differ from a native sequence bysubstitution, deletion or addition of five amino acids or fewer.Variants may also (or alternatively) be modified by, for example, thedeletion or addition of amino acids that have minimal influence on theimmunogenicity, secondary structure and hydropathic nature of thepolypeptide.

The polypeptides of the present invention can be prepared in anysuitable manner known in the art. Such polypeptides include naturallyoccurring polypeptides, recombinantly produced polypeptides,synthetically produced polypeptides, or polypeptides produced by acombination of these methods. Similarly certain embodiments disclosedherein contemplate polynucleotides comprised of the naturally occurringpolynucleotides having sugar—(e.g., ribose or deoxyribose) phosphatebackbones in 5′-to-3′ linkage, but the invention is not so limited andalso contemplates polynucleotides comprised of any of a number ofnatural and/or artificial polynucleotide analogs and/or mimetics, forexample those designed to resist degradation or having other desirablyphysicochemical properties such as synthetic polynucleotides having aphosphorothioate backbone, or the like.

Polynucleotides may comprise a native sequence (i.e., an endogenoussequence that encodes a protein or a portion thereof) or may comprise avariant, or a biological or antigenic functional equivalent of such asequence. Polynucleotide variants may contain one or more substitutions,additions, deletions and/or insertions, as further described below,preferably such that the immunogenicity of the encoded polypeptide isnot diminished, relative to a native tumor protein. The effect on theimmunogenicity of the encoded polypeptide may generally be assessed asdescribed herein. The term “variants” also encompasses homologous genesof xenogenic origin.

When comparing polynucleotide or polypeptide sequences, two sequencesare said to be “identical” if the sequence of nucleotides or amino acidsin the two sequences is the same when aligned for maximumcorrespondence, as described below. Comparisons between two sequencesare typically performed by comparing the sequences over a comparisonwindow to identify and compare local regions of sequence similarity. A“comparison window” as used herein, refers to a segment of at leastabout 20 contiguous positions, usually 30 to about 75, 40 to about 50,in which a sequence may be compared to a reference sequence of the samenumber of contiguous positions after the two sequences are optimallyaligned.

Optimal alignment of sequences for comparison may be conducted using theMegalign program in the Lasergene suite of bioinformatics software(DNASTAR, Inc., Madison, Wis.), using default parameters. This programembodies several alignment schemes described in the followingreferences: Dayhoff, M. O. (1978) A model of evolutionary change inproteins—Matrices for detecting distant relationships. In Dayhoff, M. O.(ed.) Atlas of Protein Sequence and Structure, National BiomedicalResearch Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; HeinJ. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.;Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5:151-153; Myers, E. W.and Muller W. (1988) CABIOS 4:11-17; Robinson, E. D. (1971) Comb. Theor11:105; Santou, N. Nes, M. (1987) Mol. Biol. Evol. 4:406-425; Sneath, P.H. A. and Sokal, R. R. (1973) Numerical Taxonomy—the Principles andPractice of Numerical Taxonomy, Freeman Press, San Francisco, Calif.;Wilbur, W. J. and Lipman, D. J. (1983) Proc. Natl. Acad., Sci. USA80:726-730.

Alternatively, optimal alignment of sequences for comparison may beconducted by the local identity algorithm of Smith and Waterman (1981)Add. APL. Math 2:482, by the identity alignment algorithm of Needlemanand Wunsch (1970) J. Mol. Biol. 48:443, by the search for similaritymethods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85:2444, by computerized implementations of these algorithms (GAP, BESTFIT,BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package,Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or byinspection.

One preferred example of algorithms that are suitable for determiningpercent sequence identity and sequence similarity are the BLAST andBLAST 2.0 algorithms, which are described in Altschul et al. (1977)Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol.215:403-410, respectively. BLAST and BLAST 2.0 can be used, for examplewith the parameters described herein, to determine percent sequenceidentity for the polynucleotides and polypeptides of the invention.Software for performing BLAST analyses is publicly available through theNational Center for Biotechnology Information. In one illustrativeexample, cumulative scores can be calculated using, for nucleotidesequences, the parameters M (reward score for a pair of matchingresidues; always >0) and N (penalty score for mismatching residues;always <0). For amino acid sequences, a scoring matrix can be used tocalculate the cumulative score. Extension of the word hits in eachdirection are halted when: the cumulative alignment score falls off bythe quantity X from its maximum achieved value; the cumulative scoregoes to zero or below, due to the accumulation of one or morenegative-scoring residue alignments; or the end of either sequence isreached. The BLAST algorithm parameters W, T and X determine thesensitivity and speed of the alignment. The BLASTN program (fornucleotide sequences) uses as defaults a wordlength (W) of 11, andexpectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff andHenikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915) alignments, (B) of50, expectation (E) of 10, M=5, N=−4 and a comparison of both strands.

Preferably, the “percentage of sequence identity” is determined bycomparing two optimally aligned sequences over a window of comparison ofat least 20 positions, wherein the portion of the polynucleotide orpolypeptide sequence in the comparison window may comprise additions ordeletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent,or 10 to 12 percent, as compared to the reference sequences (which doesnot comprise additions or deletions) for optimal alignment of the twosequences. The percentage is calculated by determining the number ofpositions at which the identical nucleic acid bases or amino acidresidue occurs in both sequences to yield the number of matchedpositions, dividing the number of matched positions by the total numberof positions in the reference sequence (i.e., the window size) andmultiplying the results by 100 to yield the percentage of sequenceidentity.

Therefore, the present invention encompasses polynucleotide andpolypeptide sequences having substantial identity to the sequencesdisclosed herein, for example those comprising at least 50% sequenceidentity, preferably at least 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 96%, 97%, 98%, or 99% or higher, sequence identity compared to apolynucleotide or polypeptide sequence of this invention using themethods described herein, (e.g., BLAST analysis using standardparameters, as described below). One skilled in this art will recognizethat these values can be appropriately adjusted to determinecorresponding identity of proteins encoded by two nucleotide sequencesby taking into account codon degeneracy, amino acid similarity, readingframe positioning and the like.

In additional embodiments, the present invention provides isolatedpolynucleotides and polypeptides comprising various lengths ofcontiguous stretches of sequence identical to or complementary to one ormore of the sequences disclosed herein. For example, polynucleotides areprovided by this invention that comprise at least about 15, 20, 30, 40,50, 75, 100, 150, 200, 300, 400, 500 or 1000 or more contiguousnucleotides of one or more of the sequences disclosed herein as well asall intermediate lengths there between. It will be readily understoodthat “intermediate lengths”, in this context, means any length betweenthe quoted values, such as 16, 17, 18, 19, etc.; 21, 22, 23, etc.; 30,31, 32, etc.; 50, 51, 52, 53, etc.; 100, 101, 102, 103, etc.; 150, 151,152, 153, etc.; including all integers through 200-500; 500-1,000, andthe like.

The polynucleotides of the present invention, or fragments thereof,regardless of the length of the coding sequence itself, may be combinedwith other DNA sequences, such as promoters, polyadenylation signals,additional restriction enzyme sites, multiple cloning sites, othercoding segments, and the like, such that their overall length may varyconsiderably. It is therefore contemplated that a nucleic acid fragmentof almost any length may be employed, with the total length preferablybeing limited by the ease of preparation and use in the intendedrecombinant DNA protocol. For example, illustrative DNA segments withtotal lengths of about 10,000, about 5000, about 3000, about 2,000,about 1,000, about 500, about 200, about 100, about 50 base pairs inlength, and the like, (including all intermediate lengths) arecontemplated to be useful in many implementations of this invention.

In other embodiments, the present invention is directed topolynucleotides that are capable of hybridizing under moderatelystringent conditions to a polynucleotide sequence provided herein, or afragment thereof, or a complementary sequence thereof. Hybridizationtechniques are well known in the art of molecular biology. For purposesof illustration, suitable moderately stringent conditions for testingthe hybridization of a polynucleotide of this invention with otherpolynucleotides include prewashing in a solution of 5.times. SSC, 0.5%SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50.degree. C.-65.degree. C.,5×SSC, overnight; followed by washing twice at 65.degree. C. for 20minutes with each of 2.times., 0.5.times. and 0.2.times. SSC containing0.1% SDS.

Moreover, it will be appreciated by those of ordinary skill in the artthat, as a result of the degeneracy of the genetic code, there are manynucleotide sequences that encode a polypeptide as described herein. Someof these polynucleotides bear minimal homology to the nucleotidesequence of any native gene. Nonetheless, polynucleotides that vary dueto differences in codon usage are specifically contemplated by thepresent invention. Further, alleles of the genes comprising thepolynucleotide sequences provided herein are within the scope of thepresent invention. Alleles are endogenous genes that are altered as aresult of one or more mutations, such as deletions, additions and/orsubstitutions of nucleotides. The resulting mRNA and protein may, butneed not, have an altered structure or function. Alleles may beidentified using standard techniques (such as hybridization,amplification and/or database sequence comparison).

“Polypeptides” as described herein also include combinationpolypeptides, also referred to as fusion proteins. A “combinationpolypeptide” or “fusion protein” is a polypeptide comprising at leastone of the above immunogenic portions and one or more additionalimmunogenic Leishmania sequences, which are joined via a peptide linkageinto a single amino acid chain. The sequences may be joined directly(i.e., with no intervening amino acids) or may be joined by way of alinker sequence (e.g., Gly-Cys-Gly) that does not significantly diminishthe immunogenic properties of the component polypeptides.

Fusion proteins may generally be prepared using standard techniques,including chemical conjugation. Preferably, a fusion protein isexpressed as a recombinant protein, allowing the production of increasedlevels, relative to a non-fused protein, in an expression system.Briefly, DNA sequences encoding the polypeptide components may beassembled separately, and ligated into an appropriate expression vector.The 3′ end of the DNA sequence encoding one polypeptide component isligated, with or without a peptide linker, to the 5′ end of a DNAsequence encoding the second polypeptide component so that the readingframes of the sequences are in frame. This permits translation into asingle fusion protein that retains the biological activity of bothcomponent polypeptides.

A peptide linker sequence may be employed to separate the first and thesecond polypeptide components by a distance sufficient to ensure thateach polypeptide folds into its secondary and tertiary structures. Sucha peptide linker sequence is incorporated into the fusion protein usingstandard techniques well known in the art. Suitable peptide linkersequences may be chosen based on the following factors: (1) theirability to adopt a flexible extended conformation; (2) their inabilityto adopt a secondary structure that could interact with functionalepitopes on the first and second polypeptides; and (3) the lack ofhydrophobic or charged residues that might react with the polypeptidefunctional epitopes. Preferred peptide linker sequences contain Gly, Asnand Ser residues. Other near neutral amino acids, such as Thr and Alamay also be used in the linker sequence. Amino acid sequences which maybe usefully employed as linkers include those disclosed in Maratea etal., Gene 40:39-46, 1985; Murphy et al., Proc. Natl. Acad. Sci. USA83:8258-8262, 1986; U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180.The linker sequence may generally be from 1 to about 50 amino acids inlength. Linker sequences are not required when the first and secondpolypeptides have non-essential N-terminal amino acid regions that canbe used to separate the functional domains and prevent stericinterference.

The ligated DNA sequences are operably linked to suitabletranscriptional or translational regulatory elements. The regulatoryelements responsible for expression of DNA are located only 5′ to theDNA sequence encoding the first polypeptides. Similarly, stop codonsrequired to end translation and transcription termination signals areonly present 3′ to the DNA sequence encoding the second polypeptide.

In on embodiment of the present invention fusion proteins comprise oneor more tandem repeat units. In further embodiments the one or moretandem repeat units are selected from a group consisting of SEQ ID NO.1-59. In still further embodiments, fusion proteins further comprise theantigenic portions of proteins such as, but not limited to, rK26, rK39and rLiA2, which are specifically disclosed in SEQ ID NO.'s 119-121.

Methods of Screening for Immunogenic Polypeptides

In one embodiment, the invention provides methods for screening andselecting tandem repeat proteins that may be useful in diagnosis,treatment and/or immunization of a subject or biological source such asa human patient, for example, in detecting Leishmania infection in abiological sample or in an organism, comprising: (a) constructing aLeishmania screening library; (b) screening the Leishmania screeninglibrary; and (c) analyzing the genes identified from the screening theLeishmania screening library to select genes that are tandem repeatgenes. In further embodiments, a screening library can be constructedfrom the genomic DNA of any organism, for example by way of illustrationand not limitation, an infectious or non-infectious organism, or aninfectious organism that may be pathogenic or non-pathogenic, such as abacterium, a virus, a protozoan, a fungus, a yeast, a diplomonoadid anda kinetoplastid. In certain embodiments the screening library may beconstructed from genetic material (i.e., nucleic acid) or an organismthat causes or is capable of causing leishmaniasis, such as Leishmaniainfantum, Leishmania donovani, Leishmania major, Leishmania amazonensis,Trypanosoma cruzi, or a natural or unnatural bacterial strain thatcauses leishmaniasis In a still further embodiment, libraries can beconstructed with nucleotide species, including but not limited to DNAand cDNA.

For instance, one such embodiment contemplates a method of identifyingan immunogenic polypeptide for diagnosis, treatment or immunization in apatient, comprising (a) expressing, in one or a plurality of host cells,expression products of a polynucleotide expression library whichcomprises one or a plurality of candidate immunogenicpolypeptide-encoding polynucleotides at least one of which is capable ofexpressing a candidate immunogenic polypeptide that comprises a tandemrepeat, to obtain a host cell population comprising expression products(b) contacting, under conditions and for a time sufficient for specificbinding of at least one antibody in the biological material to at leastone expression product, (i) the host cell population comprisingexpression products of (a) with (ii) a biological material that isobtained from a subject or biological source that has been infected withan infectious or non-infectious organism, or with a pathogenic ornon-pathogenic infectious organism such as a bacterium, a virus, aprotozoan, a fungus, a yeast, a diplomonoadid or a kinetoplastid, orwith a Leishmania organism or other organism that is capable of causingleishmaniasis, wherein the biological material comprises at least oneantibody and is selected from blood, serum and urine (c) detecting atleast one host cell that comprises the at least one expression productto which the at least one antibody specifically binds; (d) isolatingfrom the host cell detected in (c) a polynucleotide that encodes theexpression product to which the at least one antibody specifically bindsto obtain an isolated polynucleotide; and (e) analyzing a nucleotidesequence of the isolated polynucleotide of (d) for presence or absenceof a tandem repeat, wherein the presence of a tandem repeat indicatesthe isolated polynucleotide encodes an immunogenic polypeptide, andtherefrom identifying the immunogenic polypeptide.

Constructing a polynucleotide screening library such as a polynucleotideexpression library as described herein can be achieved by cleaving orshearing DNA with methods such as sonication or enzyme restriction,which are well known in the art. Resulting nucleotide fragments can beof any size, however, preferably averaging 1, 2, or 3 kb. Resultingnucleotide fragments are then amplified through methods that are wellknown in the art such as ligation into recombinant polynucleotidevectors including amplification and/or expression vectors and expressionwith expression vectors such as the λ phage vector or the ZAP Express©vector (Stratagene, La Jolla, Calif.), to generate a polynucleotidescreening library, for instance, a polynucleotide expression library.The screening library is then screened by exposing biological materialto host cells comprising the expressed expression library products wherethe biological material may be sera, blood, urine, saliva, or anybiological material that has been obtained from a subject or biologicalsource that has been, or is, infected by Leishmania infantum, Leishmaniadonovani, Leishmania major, Leishmania amazonensis, Trypanosoma cruzi,or other natural or unnatural strains of bacteria that causesleishmaniasis. The host cell can be a higher eukaryotic cell, such as amammalian cell (including a tumor cell), or a lower eukaryotic cell,such as a yeast cell, or the host cell can be a prokaryotic cell, suchas a bacterial cell. Representative examples of appropriate host cellsaccording to the present invention include, but need not be limited to,bacterial cells, such as E. coli, Streptomyces, Salmonella typhimurium;fungal cells, such as yeast; insect cells, such as Drosophila S2 andSpodoptera Sf9; animal cells, such as CHO, COS or 293 cells;adenoviruses; plant cells, or any suitable cell already adapted to invitro propagation or so established de novo. The selection of anappropriate host is deemed to be within the scope of those skilled inthe art from the teachings herein. Various mammalian cell culturesystems can also be employed to express recombinant protein. Examples ofmammalian expression systems include the COS-7 lines of monkey kidneyfibroblasts, described by Gluzman, Cell 23:175 (1981), and other celllines capable of expressing a compatible vector, for example, the C127,3T3, CHO, HeLa, and BHK cell lines. Mammalian expression vectors willcomprise an origin of replication, a suitable promoter and enhancer, andalso any necessary ribosome binding sites, polyadenylation site, splicedonor and acceptor sites, transcriptional termination sequences, and 5′flanking nontranscribed sequences. DNA sequences derived from the SV40splice, and polyadenylation sites may be used to provide the requirednontranscribed genetic elements. Introduction of the construct into thehost cell can be effected by a variety of methods with which thoseskilled in the art will be familiar, including but not limited to, forexample, calcium phosphate transfection, DEAE-Dextran mediatedtransfection, electroporation (e.g., Davis et al., 1986 Basic Methods inMolecular Biology) or other techniques known to the art.

Host cells expressing expression products that comprise an immunogenicpolypeptide (e.g., a polypeptide that reacts with an antibody present ina test biological material via a specific binding interaction) may beidentified according to any of a number of known methodologies. Readilyobserved host cell expression of an expression library product, forexample, resulting plaques within the expression library, can then bedetected, and the original antigenic epitope-encoding polynucleotidefragments may be excised from the expression vector and recovered. Inalternative embodiments, the screening library is derived from a subjector biological source that has been exposed to biological materialinfected by an organism (e.g., an infectious organism) such as apathogenic or non-pathogenic bacteria, protozoan, fungus, yeast, virus,a diplomonadid, a kinetoplastid or other infectious organism. Theexcised nucleotide fragments can then be sequenced using methods thatare well known in the art. In an additional embodiment these sequencesare compared to known genes, which can be found in databases such as theLeishmania infantum data gene database (GeneDB: The Wellcome TrustSanger Institute, www.genedb.org), or the GenBank gene database(National Center for Biotechnology Information (NCBI) www.ncbi.nih.gov).

The nucleotide sequences obtained from sequencing the nucleotidefragments are then analyzed to determine if these sequences comprisetandem repeats. Tandem repeats can be identified, for example, usingTandem Repeats Finder (http://tandem.bu.edu/trf/trf.htm) or othersimilar programs or methods that identify tandem repeats. Typically,these programs or methods identify the period size of the tandem repeatsand the number of copies aligned with the consensus pattern. In oneembodiment of the present invention, screening may exclude small tandemrepeat motifs that have a period size (e.g., periodicity) of about 24,21, 18, 15, 12 or 10 base pairs or less.

In yet another embodiment, sequence libraries or genomes of any organismcan be screened for tandem repeats to find epitopes that can be used forthe serodiagnosis or treatment of diseases including, but not limited toleishmaniasis, tuberculosis, HIV, and cancer. Where one or moresequences of DNA, cDNA, RNA, or amino acids of any organism are known,these sequences can be screened for tandem repeats. As described above,programs such a Tandem Repeats Finder can be used to analyze andidentify sequences that comprise tandem repeats, which are likely tocomprise epitopes that are useful in the serodiagnois or treatment of adisease. In one embodiment, the genome of L. infantum is screened fortandem repeats.

In a further embodiment, tandem repeat sequences that are identifiedfrom a sequence library are subsequently screened by exposure to abiological sample from an infected individual or blood supply toidentify tandem repeat sequences that have the greatest efficacy in theserodiagnosis or treatment of a disease.

In a still further embodiment, the tandem repeat unit or units from theidentified sequences are isolated and used to construct new proteinswith one or more tandem repeat units of one or more sequence of tandemrepeat unit. For example, among other possibilities, constructedproteins can comprise a single tandem repeat unit, multiple tandemrepeat units, or be a fusion protein with one or more tandem repeatunits, with the tandem repeat units being of different or homologoussequences.

Examples of tandem repeat units discovered through these and othermethods are disclosed in SEQ ID NO's 1-59.

In a yet further embodiment of the present invention, the tandem repeatunits or tandem repeat sequences identified by the aforementionedmethods are subsequently screened for homology to other known or unknownproteins. As used herein the term “least homology” refers to a subset ofone or more sequences that have less homology to one or more referencesequence compared to at least one sequence within the set. Referencesequences may be, for example, the sequences of polypeptides oforganisms that potentially infect organisms that are potentiallyinfected by leishmaniasis, or organisms that are potentially infected byleishmaniasis. Homology screening can be achieved by the methods ofhomology screening described above, or by the many methods that are wellknown in the art. For example, tandem repeat sequences or tandem repeatunits can be screened for homology to known parasites such as TrpanosomaCruzi, which are potentially present in patients who are being testedfor Leishmaniasis. By screening for proteins that are not homologous toproteins in such parasites, proteins can be selected for pharmaceuticalor diagnostic purposes that will have more specificity to the diseasebeing treated or tested for, which in this example is Leishmaniasis. Byscreening for proteins with high specificity to Leishmaniasis, falsepositives and misdiagnosis can be avoided.

In a still further embodiment, the tandem repeat units or tandem repeatsequences identified by the aforementioned methods are subsequentlyscreened for homology to other known or unknown proteins in mammals suchas mouse, dog or human, which are potential hosts or test hosts forLeishmaniasis. Screening for low homology to proteins in these mammalsagain allows pharmaceutical and diagnostic applications to have morespecificity to Leishmaniasis and reduces or eliminates false positivesor misdiagnosis.

In yet further embodiments, the screening methods described above can beapplied to any disease.

Compounds and Methods for Detecting Leishmania Infection

As described above, the present invention discloses methods of screeningand selecting tandem repeat proteins that have efficacy in detectingLeishmania infection in a biological sample or organism comprising thesteps: (a) constructing a Leishmania screening library; (b) screeningthe Leishmania screening library; and (c) analyzing the genes identifiedfrom the screening the Leishmania screening library to select genes thatare tandem repeat genes. Polypeptides screened and selected by this andother methods of the present invention can be used for variousapplications, including but not limited to systems and methods fordetecting, treating, preventing, monitoring and immunizing againstleishmaniasis infection in organisms or blood supplies.

Accordingly, in another embodiment of this invention, methods aredisclosed for detecting and monitoring Leishmania infection, inindividuals and blood supplies. In general, Leishmania infection may bedetected in any biological sample that contains antibodies. Preferably,the sample is blood, serum, plasma, saliva, cerebrospinal fluid orurine. More preferably, the sample is a blood or serum sample obtainedfrom a patient or a blood supply. Briefly, Leishmania infection may bedetected using one or more tandem repeat polypeptides, fusion proteinsor other polypeptides as discussed above, or variants thereof. The oneor more tandem repeat polypeptides, fusion proteins or otherpolypeptides are then used to determine the presence or absence ofantibodies that are capable of specifically binding to the polypeptideor polypeptides in the sample.

Polypeptides within the scope of the present invention include, but arenot limited to, polypeptides comprising immunogenic portions ofLeishmania antigens comprising the sequences recited in SEQ ID NO:1-59.As used herein, the term “tandem repeat” refers to a region of DNA or aprotein comprising a sequence of 4 to forty 400 nucleotides or aminoacids repeated in tandem at least two times. As used herein the term“tandem repeat unit” refers to a single unit of the sequence that isrepeated in tandem.

As used herein, references to “binding” interactions between twomolecules, such as between an antibody and its cognate antigen, mayinclude binding that may according to non-limiting theory be the resultof one or more of electrostatic interactions, hydrophobic interactions,steric interactions, van der Waals forces, hydrogen bonding or the like,or other types of interactions influencing such binding events, such asbinding of an antibody to a polypeptide, binding of a detection reagentto an antibody/peptide complex, or any other binding interaction ofmolecules, including in preferred embodiments specific bindinginteractions wherein in “specific” binding the affinity constant, Ka,may typically be less than about 10-9 M, less than about 10-8 M, lessthan about 10-7 M, less than about 10-6 M, less than about 10-5 M orless than 10-4 M.

There are a variety of assay formats known to those of ordinary skill inthe art for using a polypeptide to detect antibodies in a sample. See,e.g., Current Protocols in Immunology (Coligan et al., eds., John Wiley& Sons, publishers), and Harlow and Lane, Antibodies. A LaboratoryManual, Cold Spring Harbor Laboratory, 1988, which are incorporatedherein by reference. In a preferred embodiment, the assay involves theuse of a polypeptide (e.g., a polypeptide antigen comprising one or moretandem repeat units as described herein) immobilized on a solid supportto bind to and remove the antibody from the sample. The bound antibodymay then be detected using a detection reagent that specifically bindsto the antibody/polypeptide complex, and that comprises a readilydetectable moiety such as a detectable reporter group. Suitabledetection reagents include antibodies that bind to theantibody/polypeptide complex and free polypeptide labeled with areporter group (e.g., in a semi-competitive assay). Alternatively, acompetitive assay may be utilized, in which an antibody that binds tothe polypeptide is labeled with a reporter group and allowed to bind tothe immobilized polypeptide after incubation of the polypeptide with thesample. The extent to which components of the sample inhibit the bindingof the labeled antibody to the polypeptide is indicative of thereactivity of the sample with the immobilized polypeptide.

The solid support may be any material known to those of ordinary skillin the art to which the polypeptide may be attached. For example, thesupport may be a test well in a microtiter plate or a nitrocellulose orother suitable membrane. Alternatively, the support may be a bead ordisc, such as glass, fiberglass, latex or a plastic material such aspolystyrene or polyvinylchloride. The support may also be a magneticparticle or a fiber optic sensor, such as those disclosed, for example,in U.S. Pat. No. 5,359,681.

The polypeptide may be bound to the solid support using a variety oftechniques known to those in the art, which are amply described in thepatent and scientific literature. In the context of the presentinvention, the term “bound” refers to both noncovalent association, suchas adsorption, and covalent attachment (which may be a direct linkagebetween the antigen and functional groups on the support or may be alinkage by way of a cross-linking agent). Binding by adsorption to awell in a microtiter plate or to a membrane is preferred. In such cases,adsorption may be achieved by contacting the polypeptide, in a suitablebuffer, with the solid support for a suitable amount of time. Thecontact time varies with temperature, but is typically between about 1hour and 1 day. In general, contacting a well of a plastic microtiterplate (such as polystyrene or polyvinylchloride) with an amount ofpolypeptide ranging from about 10 ng to about 1 mu.g, and preferablyabout 100 ng, is sufficient to bind an adequate amount of antigen.Nitrocellulose will bind approximately 100 .mu.g of protein percm.sup.3.

Covalent attachment of polypeptide to a solid support may generally beachieved by first reacting the support with a bifunctional reagent thatwill react with both the support and a functional group, such as ahydroxyl or amino group, on the polypeptide. For example, thepolypeptide may be bound to a support having an appropriate polymercoating using benzoquinone or by condensation of an aldehyde group onthe support with an amine and an active hydrogen on the polypeptide(see, e.g., Pierce Immunotechnology Catalog and Handbook (1991) atA12-A13).

In certain embodiments, the assay is an enzyme linked immunosorbentassay (ELISA). This assay may be performed by first contacting apolypeptide antigen that has been immobilized on a solid support,commonly the well of a microtiter plate, with the sample, such thatantibodies to the polypeptide within the sample are allowed to bind tothe immobilized polypeptide. Unbound sample is then removed from theimmobilized polypeptide and a detection reagent capable of binding tothe immobilized antibody-polypeptide complex is added. The amount ofdetection reagent that remains bound to the solid support is thendetermined using a method appropriate for the specific detectionreagent.

Once the polypeptide is immobilized on the support, the remainingprotein binding sites on the support are typically blocked. Any suitableblocking agent known to those of ordinary skill in the art, such asbovine serum albumin (BSA) or Tween 20™ (Sigma Chemical Co., St. Louis,Mo.) may be employed. The immobilized polypeptide is then incubated withthe sample, and antibody (if present in the sample) is allowed to bindto the antigen. The sample may be diluted with a suitable diluent, suchas phosphate-buffered saline (PBS) prior to incubation. In general, anappropriate contact time (i.e., incubation time) is that period of timethat is sufficient to permit detection of the presence of antibodywithin a Leishmania-infected sample. Preferably, the contact time issufficient to achieve a level of binding that is at least 95% of thatachieved at equilibrium between bound and unbound antibody. Those ofordinary skill in the art will recognize that the time necessary toachieve equilibrium may be readily determined by assaying the level ofbinding that occurs over a period of time. At room temperature, anincubation time of about 30 minutes is generally sufficient.

Unbound sample may then be removed by washing the solid support with anappropriate buffer, such as PBS containing 0.1% Tween 20.TM. Detectionreagent may then be added to the solid support. An appropriate detectionreagent is any compound that binds to the immobilizedantibody-polypeptide complex and that can be detected by any of avariety of means known to those in the art. Preferably, the detectionreagent contains a binding agent (such as, for example, Protein A,Protein G, immunoglobulin, lectin or free antigen) conjugated to areporter group. Preferred reporter groups include enzymes (such ashorseradish peroxidase), substrates, cofactors, inhibitors, dyes,radionuclides, luminescent groups, fluorescent groups and biotin. Theconjugation of binding agent to reporter group may be achieved usingstandard methods known to those of ordinary skill in the art. Commonbinding agents may also be purchased conjugated to a variety of reportergroups from many sources (e.g., Zymed Laboratories, San Francisco,Calif. and Pierce, Rockford, Ill.).

The detection reagent is then incubated with the immobilized antibodypolypeptide complex for an amount of time sufficient to detect the boundantibody. An appropriate amount of time may generally be determined fromthe manufacturer's instructions or by assaying the level of binding thatoccurs over a period of time. Unbound detection reagent is then removedand bound detection reagent is detected using the reporter group. Themethod employed for detecting the reporter group depends upon the natureof the reporter group. For radioactive groups, scintillation counting orautoradiographic methods are generally appropriate. Spectroscopicmethods may be used to detect dyes, luminescent groups and fluorescentgroups. Biotin may be detected using avidin, coupled to a differentreporter group (commonly a radioactive or fluorescent group or anenzyme). Enzyme reporter groups may generally be detected by theaddition of substrate (generally for a specific period of time),followed by spectroscopic or other analysis of the reaction products.

To determine the presence or absence of anti-Leishmania antibodies inthe sample, the signal detected from the reporter group that remainsspecifically bound to the solid support is generally compared to asignal that corresponds to an appropriate control according toart-accepted methodologies, for example, a predetermined cut-off value.In one preferred embodiment, the cut-off value may be the average meansignal obtained when the immobilized polypeptide is incubated withsamples from an uninfected patient. In general, a sample generating asignal that is three standard deviations above the predetermined cut-offvalue is considered positive (i.e., reactive with the polypeptide). Inan alternate preferred embodiment, the cut-off value is determined usinga Receiver Operator Curve, according to the method of Sackett et al.,Clinical Epidemiology: A Basic Science for Clinical Medicine, p. 106-7(Little Brown and Co., 1985). Briefly, in this embodiment, the cut-offvalue may be determined from a plot of pairs of true positive rates(i.e., sensitivity) and false positive rates (100%-specificity) thatcorrespond to each possible cut-off value for the diagnostic testresult. The cut-off value on the plot that is the closest to the upperlefthand corner (i.e., the value that encloses the largest area) is themost accurate cut-off value, and a sample generating a signal that ishigher than the cut-off value determined by this method may beconsidered positive. Alternatively, the cut-off value may be shifted tothe left along the plot, to minimize the false positive rate, or to theright, to minimize the false negative rate.

In a related embodiment, the assay is performed in a flow-through orstrip test format, wherein the antigen (e.g., one or ore polypeptides,each comprising at least one tandem repeat unit) is immobilized on asolid support, for instance, a membrane such as nitrocellulose. In theflow-through test, the fluid sample is contacted with the solid supportunder conditions and for a time sufficient to permit antibodies, ifpresent within the sample, to bind specifically to the immobilizedpolypeptide as the sample passes through the membrane. A detectionreagent (e.g., protein A-colloidal gold) that may be present in thesolid support, or that may alternatively be applied, then binds to theantibody-polypeptide complex as the solution containing the detectionreagent flows through the membrane. Determination of bound detectionreagent may then be performed as described above. In certain relatedembodiments of the strip test format, one end of a solid supportmembrane to which the polypeptide antigen is bound, is immersed in asolution containing the sample. The sample migrates along the membranethrough a region containing detection reagent and to the area ofimmobilized polypeptide antigen. Concentration of detection reagent atthe area of the immobilized polypeptide antigen indicates the presenceof Leishmania antibodies in the sample. Typically, the concentration ofdetection reagent at that site generates a pattern, such as a line or aseries of two or more lines, which can be read visually. The absence ofsuch a pattern indicates a negative result. In general, the amount ofpolypeptide immobilized on the membrane is selected to generate avisually discernible pattern when the biological sample contains a levelof antibodies that would be sufficient to generate a positive signal inan ELISA, as discussed above. Preferably, the amount of polypeptideimmobilized on the membrane ranges from about 25 ng to about 1 .mu.g,and more preferably from about 50 ng to about 500 ng. Such tests cantypically be performed with a very small amount (e.g., one drop) ofpatient serum or blood.

Of course, numerous other assay protocols exist that are suitable foruse with the polypeptides of the present invention, and these will beknown to those familiar with the art for detecting the presence of anantibody that is capable of specifically binding to a particularpolypeptide antigen. The above descriptions are intended to be exemplaryonly.

Systems and Methods of Treating, Preventing, and Immunizing AgainstLeishmaniasis

As described above, the present invention discloses methods of screeningand selecting tandem repeat proteins that have efficacy in detectingLeishmania infection in a biological sample or organism comprising thesteps: (a) constructing a Leishmania screening library; (b) screeningthe Leishmania screening library; and (c) analyzing the genes identifiedfrom the screening the Leishmania screening library to select genes thatare tandem repeat genes. As described herein, polypeptides screened andselected by this and other methods of the present invention can be usedfor various applications, including but not limited to systems andmethods for detecting, treating, preventing, monitoring and immunizingagainst leishmaniasis infection in organisms or blood supplies.

Accordingly, in certain aspects of the present invention, described indetail below, the polypeptides, antigenic epitopes, tandem repeat units,immunogentic sequences, fusion proteins and/or soluble Leishmaniaantigens of the present invention may be incorporated intopharmaceutical compositions or vaccines. For clarity, the term“polypeptide” will be used when describing specific embodiments of theinventive therapeutic compositions and diagnostic methods; however, itwill be clear to one of skill in the art that the antigenic epitopes,polypeptides, tandem repeat units and fusion proteins of the presentinvention may also be employed in such compositions and methods.

Pharmaceutical compositions comprise one or more polypeptides, each ofwhich may contain one or more of the above sequences (or variantsthereof), and a physiologically acceptable carrier. Vaccines, alsoreferred to as immunogenic compositions, comprise one or more of theabove polypeptides and an immunostimulant, such as an adjuvant (e.g.,LbeIF4A, interleukin-12 or other cytokines) or a liposome (into whichthe polypeptide is incorporated). Many adjuvants contain a substancedesigned to protect the antigen from rapid catabolism, such as aluminumhydroxide or mineral oil, and a stimulator of immune responses, such aslipid A, Bordetella pertussis or Mycobacterium tuberculosis derivedproteins. Certain adjuvants are commercially available as, for example,Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories,Detroit, Mich.); Merck Adjuvant 65 (Merck and Company, Inc., Rahway,N.J.); AS-2 (SmithKline Beecham, Philadelphia, Pa.); aluminum salts suchas aluminum hydroxide gel (alum) or aluminum phosphate; salts ofcalcium, iron or zinc; an insoluble suspension of acylated tyrosine;acylated sugars; cationically or anionically derivatizedpolysaccharides; polyphosphazenes; biodegradable microspheres;monophosphoryl lipid A and quil A. Cytokines, such as GM-CSF,interleukin-2,-7,-12, and other like growth factors, may also be used asadjuvants.

Within certain embodiments of the invention, the adjuvant composition ispreferably one that induces an immune response predominantly of the Th1type. By virtue of its ability to induce an exclusive Th1 immuneresponse, the use of LbeIF4A, and variants thereof, as an adjuvant inthe vaccines of the present invention is particularly preferred. Certainother preferred adjuvants for eliciting a predominantly Th1-typeresponse include, for example, Imiquimod, Res-Imiquimod, a combinationof monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryllipid A, together with an aluminum salt. MPL™ adjuvants are availablefrom Corixa Corporation (Seattle, Wash.; see, for example, U.S. Pat.Nos. 4,436,727; 4,877,611; 4,866,034 and 4,912,094). CpG-containingoligonucleotides (in which the CpG dinucleotide is unmethylated) alsoinduce a predominantly Th1 response. Such oligonucleotides are wellknown and are described, for example, in WO 96/02555, WO 99/33488 andU.S. Pat. Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA sequencesare also described, for example, by Sato et al., Science 273:352, 1996.Another preferred adjuvant comprises a saponin, such as Quil A, orderivatives thereof, including QS21 and QS7 (Aquila BiopharmaceuticalsInc., Framingham, Mass.); Escin; Digitonin; or Gypsophila or Chenopodiumquinoa saponins. Other preferred formulations include more than onesaponin in the adjuvant combinations of the present invention, forexample combinations of at least two of the following group comprisingQS21, QS7, Quil A, .beta.-escin, or digitonin.

Alternatively the saponin formulations may be combined with vaccinevehicles composed of chitosan or other polycationic polymers,polylactide and polylactide-co-glycolide particles, poly-N-acetylglucosamine-based polymer matrix, particles composed of polysaccharidesor chemically modified polysaccharides, liposomes and lipid-basedparticles, particles composed of glycerol monoesters, etc. The saponinsmay also be formulated in the presence of cholesterol to formparticulate structures such as liposomes or ISCOMs. Furthermore, thesaponins may be formulated together with a polyoxyethylene ether orester, in either a non-particulate solution or suspension, or in aparticulate structure such as a paucilamelar liposome or ISCOM. Thesaponins may also be formulated with excipients such as Carbopol.sup.Rto increase viscosity, or may be formulated in a dry powder form with apowder excipient such as lactose.

In one preferred embodiment, the adjuvant system includes thecombination of a monophosphoryl lipid A and a saponin derivative, suchas the combination of QS21 and 3D-MPL™ adjuvant, as described in WO94/00153, or a less reactogenic composition where the QS21 is quenchedwith cholesterol, as described in WO 96/33739. Other preferredformulations comprise an oil-in-water emulsion and tocopherol. Anotherparticularly preferred adjuvant formulation employing QS21, 3D-MPL™adjuvant and tocopherol in an oil-in-water emulsion is described in WO95/17210.

Another enhanced adjuvant system involves the combination of aCpG-containing oligonucleotide and a saponin derivative particularly thecombination of CpG and QS21 is disclosed in WO 00/09159. Preferably theformulation additionally comprises an oil in water emulsion andtocopherol.

Additional illustrative adjuvants for use in the compositions of theinvention include Montanide ISA 720 (Seppic, France), SAF (Chiron,Calif., United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series ofadjuvants (e.g., SBAS-2 or SBAS-4, available from SmithKline Beecham,Rixensart, Belgium), EnhanZyn.TM. (Corixa, Hamilton, Mont.), RC-529(Corixa, Hamilton, Mont.) and other aminoalkyl glucosaminide4-phosphates (AGPs), such as those described in U.S. Pat. No. 6,113,918and pending U.S. patent application Ser. No. 09/074,720, the disclosuresof which are incorporated herein by reference in their entireties, andpolyoxyethylene ether adjuvants such as those described in WO99/52549A1.

Other preferred adjuvants include adjuvant molecules of the generalformula (I): HO(CH.sub.2CH.sub.20).sub.n-A-R, wherein, n is 1-50, A is abond or —C(O)—, R is C.sub.1-50 alkyl or Phenyl C.sub.1-50 alkyl. Oneembodiment of the present invention consists of a vaccine formulationcomprising a polyoxyethylene ether of general formula (I), wherein n isbetween 1 and 50, preferably 4-24, most preferably 9; the R component isC.sub.1-50, preferably C.sub.4-C.sub.20 alkyl and most preferablyC.sub.12 alkyl, and A is a bond. The concentration of thepolyoxyethylene ethers should be in the range 0.1-20%, preferably from0.1-10%, and most preferably in the range 0.1-1%. Preferredpolyoxyethylene ethers are selected from the following group:polyoxyethylene-9-lauryl ether, polyoxyethylene-9-steoryl ether,polyoxyethylene-8-steoryl ether, polyoxyethylene-4-lauryl ether,polyoxyethylene-35-lauryl ether, and polyoxyethylene-23-lauryl ether.Polyoxyethylene ethers such as polyoxyethylene lauryl ether aredescribed in the Merck index (12.sup.th edition: entry 7717). Theseadjuvant molecules are described in WO 99/52549. The polyoxyethyleneether according to the general formula (I) above may, if desired, becombined with another adjuvant. For example, a preferred adjuvantcombination is preferably with CpG as described in the pending UK patentapplication GB 9820956.2.

Vaccines may additionally contain a delivery vehicle, such as abiodegradable microsphere (disclosed, for example, in U.S. Pat. Nos.4,897,268 and 5,075,109). Pharmaceutical compositions and vaccineswithin the scope of the present invention may also contain otherLeishmania antigens, either incorporated into a combination polypeptideor present within one or more separate polypeptides.

Alternatively, a pharmaceutical or immunogenic composition may containan immunostimulant, such as an adjuvant (e.g., LbeIF4A, interleukin-12or other cytokines, or DNA coding for such enhancers), and apolynucleotide (e.g., DNA) encoding one or more of the polypeptides orfusion proteins described above, such that the polypeptide is generatedin situ. In such compositions, the DNA may be present within any of avariety of delivery systems known to those of ordinary skill in the art,including nucleic acid expression systems, bacteria and viral expressionsystems. Appropriate nucleic acid expression systems contain thenecessary DNA sequences for expression in the patient (such as asuitable promoter and terminating signal). Bacterial delivery systemsinvolve the administration of a bacterium (such asBacillus-Calmette-Guerrin) that expresses an immunogenic portion of thepolypeptide on its cell surface. In a preferred embodiment, the DNA maybe introduced using a viral expression system (e.g., vaccinia or otherpox virus, retrovirus, or adenovirus), which may involve the use of anon-pathogenic (defective), replication competent virus. Techniques forincorporating DNA into such expression systems are well known to thoseof ordinary skill in the art. The DNA may also be “naked,” as described,for example, in Ulmer et al., Science 259:1745-1749 (1993) and reviewedby Cohen, Science 259:1691-1692 (1993). The uptake of naked DNA may beincreased by coating the DNA onto biodegradable beads, which areefficiently transported into the cells.

While any suitable carrier known to those of ordinary skill in the artmay be employed in the pharmaceutical compositions of this invention,the type of carrier will vary depending on the mode of administration.For parenteral administration, such as subcutaneous injection, thecarrier preferably comprises water, saline, alcohol, a fat, a wax or abuffer. For oral administration, any of the above carriers or a solidcarrier, such as mannitol, lactose, starch, magnesium stearate, sodiumsaccharine, talcum, cellulose, glucose, sucrose, and magnesiumcarbonate, may be employed. Biodegradable microspheres (e.g., polylacticgalactide) may also be employed as carriers for the pharmaceuticalcompositions of this invention. Suitable biodegradable microspheres aredisclosed, for example, in U.S. Pat. Nos. 4,897,268 and 5,075,109.

In one preferred embodiment, compositions of the present inventioninclude multiple polypeptides selected so as to provide enhancedprotection against a variety of Leishmania species. Such polypeptidesmay be selected based on the species of origin of the native antigen orbased on a high degree of conservation of amino acid sequence amongdifferent species of Leishmania. A combination of individualpolypeptides may be particularly effective as a prophylactic and/ortherapeutic vaccine because (1) stimulation of proliferation and/orcytokine production by a combination of individual polypeptides may beadditive, (2) stimulation of proliferation and/or cytokine production bya combination of individual polypeptides may be synergistic, (3) acombination of individual polypeptides may stimulate cytokine profilesin such a way as to be complementary to each other and/or (4) individualpolypeptides may be complementary to one another when certain of themare expressed more abundantly on the individual species or strain ofLeishmania responsible for infection. A preferred combination containspolypeptides that comprise immunogenic portions of M15, Ldp23, Lbhsp83,Lt-1 and LbeIF4A. Alternatively, or in addition, the combination mayinclude one or more polypeptides comprising immunogenic portions ofother Leishmania antigens disclosed herein, and/or soluble Leishmaniaantigens.

In another preferred embodiment, compositions of the present inventioninclude single polypeptides selected so as to provide enhancedprotection against a variety of Leishmania species. A single individualpolypeptide may be particularly effective as a prophylactic and/ortherapeutic vaccine for those reasons stated above for combinations ofindividual polypeptides.

In another embodiment, compositions of the present invention includeindividual polypeptides and combinations of the above describedpolypeptides employed with a variety of adjuvants, such as IL-12(protein or DNA) to confer a protective response against a variety ofLeishmania species.

In yet another embodiment, compositions of the present invention includeDNA constructs of the various Leishmania species employed alone or incombination with variety of adjuvants, such as IL-12 (protein or DNA) toconfer a protective response against a variety of Leishmania species.

The above pharmaceutical compositions and vaccines may be used, forexample, to induce protective immunity against Leishmania in a patient,such as a human or a dog, to prevent leishmaniasis. Appropriate dosesand methods of administration for this purposes are described in detailbelow.

The pharmaceutical and immunogenic compositions described herein mayalso be used to stimulate an immune response, which may be cellularand/or humoral, in a patient. For Leishmania-infected patients, theimmune responses that may be generated include a preferential Th1 immuneresponse (i.e., a response characterized by the production of thecytokines interleukin-1, interleukin-2, interleukin-12 and/orinterferon-.gamma., as well as tumor necrosis factor-.alpha.). Foruninfected patients, the immune response may be the production ofinterleukin-12 and/or interleukin-2, or the stimulation of gamma deltaT-cells. In either category of patient, the response stimulated mayinclude IL-12 production. Such responses may also be elicited inbiological samples of PBMC or components thereof derived fromLeishmania-infected or uninfected individuals. As noted above, assaysfor any of the above cytokines may generally be performed using methodsknown to those of ordinary skill in the art, such as an enzyme-linkedimmunosorbent assay (ELISA).

Suitable pharmaceutical compositions and vaccines for use in this aspectof the present invention are those that contain at least one polypeptidecomprising an immunogenic portion of a Leishmania antigen disclosedherein (or a variant thereof). Preferably, the polypeptides employed inthe pharmaceutical compositions and vaccines are complementary, asdescribed above. Soluble Leishmania antigens, with or without additionalpolypeptides, may also be employed.

The pharmaceutical compositions and vaccines described herein may alsobe used to treat a patient afflicted with a disease responsive to IL-12stimulation. The patient may be any warm-blooded animal, such as a humanor a dog. Such diseases include infections (which may be, for example,bacterial, viral or protozoan) or diseases such as cancer. In oneembodiment, the disease is leishmaniasis, and the patient may displayclinical symptoms or may be asymptomatic. In general, the responsivenessof a particular disease to IL-12 stimulation may be determined byevaluating the effect of treatment with a pharmaceutical composition orvaccine of the present invention on clinical correlates of immunity. Forexample, if treatment results in a heightened Th1 response or theconversion of a Th2 to a Th1 profile, with accompanying clinicalimprovement in the treated patient, the disease is responsive to IL-12stimulation. Polypeptide administration may be as described below, ormay extend for a longer period of time, depending on the indication.Preferably, the polypeptides employed in the pharmaceutical compositionsand vaccines are complementary, as described above. A particularlypreferred combination contains polypeptides that comprise immunogenicportions of LmSTI1, Ldp23, Lbhsp83, Lt-1 and LbeIF4A, Lmsp1a, Lmsp9a,and TSA. Soluble Leishmania antigens, with or without additionalpolypeptides, may also be employed.

Routes and frequency of administration, as well as dosage, for the aboveaspects of the present invention will vary from individual to individualand may parallel those currently being used in immunization againstother infections, including protozoan, viral and bacterial infections.In general, the pharmaceutical compositions and vaccines may beadministered by injection (e.g., intracutaneous, intramuscular,intravenous or subcutaneous), intranasally (e.g., by aspiration) ororally. Between 1 and 12 doses may be administered over a 1 year period.For therapeutic vaccination (i.e., treatment of an infected individual),12 doses are preferably administered, at one month intervals. Forprophylactic use, 3 doses are preferably administered, at 3 monthintervals. In either case, booster vaccinations may be givenperiodically thereafter. Alternate protocols may be appropriate forindividual patients. A suitable dose is an amount of polypeptide or DNAthat, when administered as described above, is capable of raising animmune response in an immunized patient sufficient to protect thepatient from leishmaniasis for at least 1-2 years. In general, theamount of polypeptide present in a dose (or produced in situ by the DNAin a dose) ranges from about 100 ng to about 1 mg per kg of host,typically from about 10 .mu.g to about 100 .mu.g. Suitable dose sizeswill vary with the size of the patient, but will typically range fromabout 0.1 mL to about 5 mL.

In another aspect, this invention provides methods for using one or moreof the polypeptides described above to diagnose Leishmania infection ina patient using a skin test. As used herein, a “skin test” is any assayperformed directly on a patient in which a delayed-type hypersensitivity(DTH) reaction (such as induration and accompanying redness) is measuredfollowing intradermal injection of one or more polypeptides as describedabove. Such injection may be achieved using any suitable devicesufficient to contact the polypeptide or polypeptides with dermal cellsof the patient, such as a tuberculin syringe or 1 mL syringe.Preferably, the reaction is measured at least 48 hours after injection,more preferably 72 hours after injection.

The DTH reaction is a cell-mediated immune response, which is greater inpatients that have been exposed previously to a test antigen (i.e., animmunogenic portion of a polypeptide employed, or a variant thereof).The response may be measured visually, using a ruler. In general,induration that is greater than about 0.5 cm in diameter, preferablygreater than about 1.0 cm in diameter, is a positive response,indicative of Leishmania infection, which may or may not be manifestedas an active disease.

The polypeptides of this invention are preferably formulated, for use ina skin test, as pharmaceutical compositions containing at least onepolypeptide and a physiologically acceptable carrier, as describedabove. Such compositions typically contain one or more of the abovepolypeptides in an amount ranging from about 1 .mu.g to 100 .mu.g,preferably from about 10 .mu.g to 50 .mu.g in a volume of 0.1 mL.Preferably, the carrier employed in such pharmaceutical compositions isa saline solution with appropriate preservatives, such as phenol and/orTween .sub.80T.

The inventive polypeptides may also be employed in combination with oneor more known Leishmania antigens in the diagnosis of leishmaniasis,using, for example, the skin test described above. Preferably,individual polypeptides are chosen in such a way as to be complementaryto each other. Examples of known Leishmania antigens which may beusefully employed in conjunction with the inventive polypeptides includeK39 (Burn et al., Proc. Natl. Acad. Sci. USA, 1993 90:775-779).

The following examples are offered by way of illustration, and not byway of limitation.

EXAMPLES Example 1 Parasite and Infection of Hamsters

Leishmania infantum, Leishmania donovani, Leishmania major, Leishmaniaamazonensis and Trypanosoma cruzi were used to infect Hamsters andthereby produce infected sera. Hamsters were infected intracardiacallywith 1×10⁷ Leishmania infantum, Leishmania donovani, Leishmania major,Leishmania amazonensis or Trypanosoma cruzi promastigotes in astationary phase. After eight to twelve weeks the infected hamsters weresacrificed and the sera were collected.

Example 2 Patient Sera

Sudanese visceral leishmaniasis patient sera were collected frompatients with active disease diagnosed clinically and provenparasitologically. Patient sera of cutaneous leishmaniasis (Brazil),tuberculosis (USA) and malaria (Brazil) were collected fromwell-characterized patients, including parasitological diagnosis(cutaneous leishmaniasis, malaria) or culture positive diagnosis(tuberculosis). Normal sera were obtained from healthy individuals inthe United States.

Example 3 Serological Screening of L. infantum Expression Library

Construction and screening of library was performed. In brief, total DNAfrom L. infantum was randomly sheared by sonication to an average sizeof ˜2 kb, blunt ended with T4 DNA polymerase, and followed by theaddition of EcoRI adaptors. The insert was subsequently ligated into theZAP Express© vector predigested with EcoRI (Stratagene, La Jolla,Calif.) and packaged using Gigapack III© Gold Packaging Extract(Stratagene). The phage library was amplified and then screenedaccording to the manufacturer's instruction with pooled L.infantum-infected hamster sera or pooled Sudanese visceral leishmaniasispatient sera described above. Approximately 5×10⁵ plaques were screenedusing the sera at a dilution of 1:100 and immunoreactive plaques weredetected with the alkaline phosphatase-conjugated goat anti-hamster IgGor goat anti-human IgG (KPL, Gaithersburg, Md.) and the substrate,BCIP/NBT (KPL). PBK-CMV phagemid vectors were excised from theimmunoreactive phage clones according to the manufacturer's protocol.The inserts were sequenced and analyzed using Leishmania infantum genedatabase (GeneDB: The Wellcome Trust Sanger Institute, www.genedb.org).

Example 4 Tandem Repeat Gene Analysis

The genes identified by the screening were analyzed to determine whetherthey are tandem repeat genes. Tandem Repeats Finder, a program to locateand display tandem repeats in DNA sequences, was used for this analysistandem.bu.edu/trf/trf.html). As a control for the screened genes, 108genes which were randomly picked from the L. infantum gene database werealso analyzed for the presence of tandem repeat motifs. The programcalculates the score according to the nature of the tandem repeat genessuch as the period size of the repeat, the number of copies aligned withthe consensus pattern and the percent of matches between adjacent copiesoverall. In this study the genes were regarded as tandem repeat genes ifthe scores from the Tandem Repeats Finder analysis were higher than 500,thus excluding genes containing small tandem repeat motifs such asLinJ01.0470 and LinJ13.0810 (Table I).

TABLE I L. infantum proteins identified by serological screening GENE DBTR analysis ID Gene Size PS CN Score LinJ01.0470 hypothetical protein151 3 11 66 LINJ03.0120 hypothetical protein 237 117 31.8 7033LinJ05.0380 microtubule-associated protein 165 114 28.5 6336 LinJ05.0590hypothetical protein 86 LinJ08.0860 mitochondrial DNA polymerasebeta-PAK 154 LinJ08.1010 stress-induced protein sti1 62 LinJ08.1130hypothetical protein 50 LinJ10.1460 hypothetical protein 56 LinJ13.0810hypothetical protein 76 15 3.7 74 LinJ14.1160 kinesin K39 (rK39) 241 11727.9 5237 LinJ14.1190 kinesin K39 95 105 6.2 1198 LinJ14.1540hypothetical protein 112 72 6.1 806 LinJ15.0490 tb-292 membraneassociated protein-like 164 105 31.6 6027 LinJ16.1540 kinesin 230 42138.5 10588 LinJ16.1560 kinesin 88 42 2.5 172 LinJ16.1750 hypotheticalprotein 346 219 8.7 3691 LinJ17.0100 elongation factor 1-alpha 49LinJ17.0610 hypothetical protein 86 LinJ18.0610 hypothetical protein 68LinJ18.1150 hypothetical protein 107 LinJ21.0440 1a RNA binding protein37 LinJ22.0680 hypothetical protein 45 30 34.2 1137 LinJ22.1590hypothetical protein 234 84 29.2 3993 LinJ24.1570 basal body component164 LinJ26.0980 dynein heavy chain 458 LinJ26.1200 Hsp70.4 heat shockprotein 70 70 LinJ27.0290 nucleoporin 159 27 2.4 74 LinJ27.0410calpain-like cysteine peptidase 702 12 2.6 53 LinJ27.1480 hypotheticalprotein 247 LinJ28.2310 glycoprotein 96-92 61 315 2.2 1398 LinJ28.3170hypothetical protein 75 60 23.4 2546 LinJ31.0530 amastin 21 LinJ31.1430hypothetical protein 95 LinJ32.2730 hypothetical protein 173 150 10.32916 LinJ32.2780 membrane associated protein 131 30 60.9 3125LinJ33.2870 hypothetical protein 413 444 7 6041 LinJ34.0710 hypotheticalprotein 306 168 16.3 4487 LinJ34.2140 hypothetical protein 296 249 7.43604 LinJ35.0590 proteophosphoglycan ppg4 536 45 246.1 10667 LinJ35.0600proteophosphoglycan ppg3 — 135 37.8 8773 LinJ35.4250 poly(A) bindingprotein 65 36 3.6 111 LinJ36.4560 chaperonin Hsp60, mitochondrial 59LinJ36.4930 sterol 24-c-methyltransferase 40

ID numbers in GeneDB are temporary and may vary. Sizes are shown in kDa.Data of PS, CN and score in TR analysis are from a program analysisusing Tandem Repeats Finder. Tandem repeat genes are shown in boldletters. Blanks in PS, CN and Score columns represent no repeat found inthe genes. PS: period size (bp) of the repeat, CN: number of copiesaligned with the consensus pattern.

Example 5 PCR Analysis and Cloning of Tandem Repeat Genes

Tandem repeat sequences of LinJ16.1750, LinJ22.1590 or LinJ33.2870 wereamplified by PCR using primers corresponding to both ends of a singlecopy of the tandem repeat (primer sequences are shown in Table II). Theentire gene sequence of LinJ28.2310 was amplified by PCR and primersused for this reaction are also shown in Table II. To analyze whether ornot those genes are conserved among Leishmania species, total DNA of L.infantum, L. donovani, L. major, L. amazonensis and Trypanosoma cruziwere used as templates. As a control, a T. cruzi gene (GenBank:XM_(—)810936) was amplified by PCR using L. infantum and Trypanosomacruzi DNA as templates (primer sequence in Table II). For the cloning ofthe genes for producing recombinant proteins, L. infantum total DNA wasused as a template for the PCR reactions.

TABLE II Primers used in this study Gene Primer sequence LinJ16.1750/CAA TTA CAT ATG TAC CCG TTC CTA CGG SEQ ID NO: 122 CTG CAA TTA GGA TCCCTA GCG CGA CGC CAG CTC GTC LinJ22.1590/ CAA TTA CAT ATG GCT GAC CTG AGGGAG SEQ ID NO: 123 CAG CAA TTA GGA TCC CTA CAC CTC GGC GTC CCT GTCLinJ28.2310/ CAA TTA CAT ATG AGC GCT GCA CCG TCC SEQ ID NO: 124 CAA TTAGAA TTC CTA CGC AAG TCC GAG GGC LinJ33.2870/ CAA TTA CAT ATG CAG CGG CTGGTG CTC SEQ ID NO: 125 CAA TTA GGA TCC CTA CGA CGT CCG CGG CAG CGC T.cruzi CAA TTA CAT ATG TGC ATT GCT CTT GGC XM_810936/ ATCGTC CAA TTA AAGCTT CTG GGG CGT SEQ ID NO: 126 GAA GCG TAT GTA CTC

Example 6 Expression of Recombinant Proteins

The PCR product corresponding to two copies of LinJ16.1750 repeat(LinJ16.1750r2), three copies of LinJ22.1590 repeat (LinJ22.1590r3), acopy of LinJ33.2870 repeat (LinJ33.2870r1) or an entire gene ofLinJ28.2310 was inserted into NdeI/BamHI or NdeI/EcoRI site of pET28vector. The sequence of the inserts was then analyzed. These pET28vectors were transformed into E. coli Rosetta for expression of therecombinant proteins. Expression of the recombinant proteins was inducedby cultivation with 1M isopropyl-β-D-thiogalactoside. The recombinantproteins were then purified as 6×His-tagged proteins using Ni-NTAagarose (Qiagen Inc., Valencia, Calif.). Purity of the proteins wasassessed by Coomassie blue-staining following SDS-PAGE. Theconcentrations of these proteins were measured by BCA protein assay(Pierce Biotechnology Inc., Rockford, Ill.).

Example 7 Enzyme-Linked Immunosorbent Assay (ELISA)

rLinJ16.1750r2, rLinJ22.1590r3, rLinJ28.2310, rLinJ33.2870, rK39 or L.infantum promastigote soluble lysate antigen (LiSLA) were diluted inELISA coating buffer, and 96-well plates were coated withrLinJ16.1750r2, rLinJ22.1590r3, rLinJ28.2310, rLinJ33.2870 (200 ng),rK39 (50 ng) or LiSLA (1 μg) followed by blocking withphosphate-buffered saline containing 0.05% Tween-20 and 1% bovine serumalbumin. Next, the plates were incubated with patient sera (diluted1:100) as well as healthy controls and then with horseradishperoxidase-conjugated protein G (Zymed laboratories, South SanFrancisco, Calif.). The plates were developed with TMB peroxidasesubstrate (KPL) and read by a microplate reader at a 450 nm wavelength.

Example 8 Detection of Tandem Repeat Genes in Serologically ScreenedGenes

Pooled sera from L. infantum-infected hamsters or Sudanese visceralleishmaniasis patients were used to screen a L. infantum expressionlibrary. A half million plaques covering about eight times L. infantumgenomic equivalents were screened. PBK-CMV phagemids were excised frompositive clones; the inserts were sequenced and analyzed using GeneDB. Atotal of 43 genes were identified as genes encoding B-cell antigens(Table I). Some of the genes encoded previously identified antigens suchas HSP70 and K39, but most of them encoded previously unidentifiedantigens.

The genes identified by the screening were then analyzed by TandemRepeats Finder. In this study, a gene was regarded as a tandem repeatgene if a score from the analysis was 500 or higher thereby excludinggenes containing small tandem repeat domains. Of the 43 genes identifiedby the serological screening, 19 genes were identified as tandem repeatgenes (Table I). For example, LinJ16.1750 contained 8.7 copies of a 219bp sequence and LinJ28.3170 contained 23.4 copies of a 60 bp sequence.With the exception of LinJ14.1160 (known as rK39), these genes werenewly identified as genes encoding B-cell antigens. One hundred andeight genes, which were picked randomly from the database (3 genes fromeach chromosome), were also analyzed with Tandem Repeats Finder tocompare the prevalence of tandem repeat genes with that in the genesidentified by screening. In contrast to the screened genes, no tandemrepeat genes were found in the 108 randomly picked genes.

Example 9 PCR Analysis of Tandem Repeat Genes

PCR amplifications were performed with total DNA from Leishmania speciesand T. cruzi to analyze whether or not tandem repeat genes wereconserved among these parasites. Using sets of primers specific fortandem repeat domains of LinJ16.1750 and LinJ22.1590, the PCR productsshowed ladder bands corresponding to one or multiple copies of therepeat (FIG. 1). These genes were conserved among Leishmania speciesbecause similar band patterns were observed through all four Leishmaniaspecies tested. When primers for tandem repeat domains of LinJ33.2870were used, the PCR product also showed bands which sizes corresponded toone or two copies of the repeat in Leishmania species, but not in L.amazonensis (FIG. 1). When primers for the whole gene of LinJ33.2870were used, a 1.5 kb band was found in L. infantum and L. donovani, andbands of 2.1 kb and 1.8 kb were found in L. major and L. amazonensis,respectively. In all cases, no bands were found in PCR reactions usingT. cruzi DNA. In contrast, a single band with an expected size was foundin T. cruzi but not in L. infantum when primers for a T. cruzi gene wereused for PCR. Thus, while the tandem repeat genes are not conservedbetween Leishmania and T. cruzi, they are well conserved betweenLeishmania spp.

Example 10 Recognition of Recombinant Tandem Repeat Proteins by VisceralLeishmaniasis Patient Sera

To formally test the identified tandem repeat proteins as potentialdiagnostic candidates, LinJ16.1750r2, LinJ22.1590r3, LinJ28.2310 andLinJ33.2870r1 were expressed as recombinant proteins (FIG. 2).

The prevalence of antibodies to the recombinant proteins in apreliminary screen of ten Sudanese visceral leishmaniasis patient seraby ELISA. The visceral leishmaniasis patient sera showed significantlystronger reactivity to all the recombinant proteins than sera from thegroups without visceral leishmaniasis, i.e. tuberculosis, malaria andcutaneous leishmaniasis patients or healthy individuals, despite thefinding that cutaneous leishmaniasis patients showed antibody responsesto LiSLA (FIG. 3). Among the tested proteins, rLinJ16.1750r2 was thebest antigen recognized strongly by visceral leishmaniasis patient serawith a high degree of specificity. Next, rLinJ16.1750r2 was tested withadditional Sudanese visceral leishmaniasis patient sera. Among 35 seratested, 34 showed antibody responses to rLinJ16.1750r2 (the cutoff valuewas the mean+3 SD of healthy controls: FIG. 4). The sensitivity usingrLinJ16.1750r2 was 97%, comparable to that of rK39 (35/35, 100%: FIG.4). Mean O.D. values to rLinJ16.1750r2 and rK39 were 1.159 and 1.771,respectively.

Although these 35 sera were 100% positive using rK39, eight sera showedlow reactivity to rK39 (OD values were <1.0: FIG. 4). These eightsamples were tested for reactivity to rLinJ16.1750r2, rLinJ22.1590r3,rLinJ28.2310 or rLinJ33.2870r1 to examine whether or not those antigenscould complement rK39 for more sensitive antibody detection. Five of theeight sera showed better responses to the new antigens than to rK39 (No.3-7 in FIG. 5). Five patients (No. 3-7) showed better responses torLinJ22.1590r3, four (No. 4-7) to rLinJ28.2310, and three (No. 3, 5 and6) to rLinJ33.2870r1. rLinJ22.1590r3 was recognized weakly by all theeight sera compared to rK39.

DNA sequences of 8,191 L. infantum genes were obtained from L. infantumGeneDB www.genedb.org/genedb/linfantum/index.jsp). Tandem RepeatsFinder, a program used to locate and display tandem repeats in DNAsequences, was used for this analysis tandem.bu.edu/trf/trf.html). Theprogram calculates the score according to the nature of the tandemrepeat genes such as the period size of the repeat, the number of copiesaligned with the consensus pattern and the percent of matches betweenadjacent copies overall. Thus, an output of a high score in geneanalysis means the gene possesses a large tandem repeat sequence and therepeat is highly conserved among the copies. A low score means theopposite; for example, a score of a gene with 3.6 copies of a 36 byrepeat was 111. In this study, the genes were regarded as tandem repeatgenes if the scores from the Tandem Repeats Finder analysis were higherthan 500, thus excluding genes containing small tandem repeat motifs.Using these screening parameters, the following genes were identifiedfrom the L. infantum GeneDB. (Table 3)

TABLE III L. infantum TR genes identified by Tandem Repeats Finder SizePS3 Gene ID1 C/I2 Product (kDa) (bp) CN3 Score3 Ref4 LinJ03.0120 Chypothetical protein 237 117 31.8 7033 1 LinJ05.0340 C viscerotropicleishmaniasis antigen 95 99 13.8 2545 2 LinJ05.0380 Cmicrotubule-associated protein 165 114 28.5 6336 1 LinJ09.0950 Cpolyubiquitin 74 228 8 3621 LinJ11.0070 C hypothetical protein 147 13812.9 2435 LinJ13.0780 C hypothetical protein 107 63 14.2 1637LinJ14.0370 C hypothetical protein 302 84 10.9 1475 LinJ14.1160 Ckinesin K39 242 117 27.9 5237 1, 3 LinJ14.1180 I kinesin K39 278 168 8.22671 LinJ14.1190 I kinesin K39 95 315 6.1 2828 1 LinJ14.1200 C kinesinK39 79 468 3.4 1971 3 LinJ14.1210 I kinesin K39 337 483 10.9 3676LinJ14.1540 C hypothetical protein 112 72 6.1 806 1 LinJ15.0490 I tb-292membrane associated 105 31.6 6027 1 LinJ15.1570 I 112 105 29.9 5588LinJ16.1540 C kinesin 230 42 138.5 10588 1 LinJ16.1750 C hypotheticalprotein 346 219 8.7 3691 1 LinJ18.1030 C Hypothetical repeat protein 4621 30.4 1036 LinJ19.0940 C 24 6 95 1076 LinJ19.1560 I 166 81 21.1 3094LinJ20.1220 C calpain-like cysteine peptidase 112 39 11.3 826LinJ21.2010 C hypothetical protein 306 192 5.3 2003 LinJ22.0410 Chypothetical protein 130 183 15.9 5779 LinJ22.0680 C hypotheticalprotein 45 216 5.9 1240 1, 4 LinJ22.1510 C hypothetical protein 179 8113.5 1984 LinJ22.1520 C 72 39 42.9 3197 LinJ22.1550 C 126 81 10.4 1504LinJ22.1560 I 172 267 16.9 8614 LinJ22.1570 C 210 81 23.5 3230LinJ22.1580 C 175 267 17.1 8591 LinJ22.1590 C hypothetical protein 23484 29.2 3993 1 LinJ23.1180 C hydrophilic surface protein (HASPB) 26 4211.2 832 5 LinJ25.1100 C hypothetical protein 91 66 9.5 1142 LinJ25.1910C hypothetical protein 91 369 2 1443 LinJ26.2140 C hypothetical protein215 48 63.4 5289 LinJ27.0140 I kinetoplast-associated protein-like 33 3019.9 1086 LinJ27.0170 C kinetoplast-associated protein-like 95 30 62.13283 LinJ27.0400 C calpain-like cysteine peptidase 687 204 43.8 17362LinJ28.2310 C glycoprotein 96-92 61 315 2.2 1398 1 LinJ28.3170 Chypothetical protein 75 60 23.4 2546 1 LinJ29.0110 C hypotheticalprotein 278 24 28.6 967 LinJ30.0400 C hypothetical protein 56 117 7.41716 LinJ31.1820 C hypothetical protein 49 75 4.1 581 LinJ31.1840 Chypothetical protein 52 24 18.1 814 LinJ31.2660 C hypothetical protein247 456 2.2 1973 LinJ31.3360 C hypothetical protein 71 30 11.1 556LinJ32.2730 C hypothetical protein 173 150 10.3 2916 1 LinJ32.2780 Cmembrane associated protein-like 132 30 60.9 3125 1 LinJ32.3710 Chypothetical protein 292 99 3.9 730 LinJ33.2870 C hypothetical protein413 444 7 6041 1 LinJ34.0710 I hypothetical protein 336 9.5 4517 1LinJ34.2140 C hypothetical protein 296 249 7.4 3604 1 LinJ34.4250 Chypothetical protein 168 168 6.1 1960 LinJ35.0590 C proteophosphoglycanppg4 536 45 246.1 10667 1 LinJ35.0600 I proteophosphoglycan ppg3 13537.8 8773 1 LinJ35.0610 C proteophosphoglycan ppg4 291 45 183.2 13275LinJ35.0620 I proteophosphoglycan 5 495 90 152.5 15050 LinJ35.0630 Iproteophosphoglycan ppg4 281 45 176.6 10813 LinJ35.0640 I hypotheticalprotein 95 45 58.4 4766 LinJ35.1530 C hypothetical protein 328 141 2.4661 LinJ35.1620 I hypothetical protein 126 8.7 1855 LinJ35.4500 Chypothetical protein 60 165 4.5 1438 LinJ36.0320 C histidine secretoryacid phosphatase 71 72 6.5 861 LinJ36.5810 C hypothetical protein 365276 4.3 2341

The following notes correspond to the superscript notes in Table III:(1) ID numbers in GeneDB are temporary and may vary; (2) C or I mean thegene is a complete or incomplete gene, respectively; (3) Data of PS, CNand score in TR analysis are from a program analysis using TandemRepeats Finder. TR genes are shown in bold letters. Blanks in PS, CN andScore columns represent no repeat found in the genes. PS: period size(bp) of the repeat, CN: number of copies aligned with the consensuspattern; and (4) antigenicity of the protein has been reported in thereferenced paper.

Example 12 Analysis of Amino Acid Compositions of Tandem Repeat Proteins

Tandem repeat proteins, which encoded by the tandem repeat genesidentified by the bioinformatic analysis, were analyzed their isometricpoints and amino acid compositions using a software, EditSeq (DNASTARInc., Madison, Wis.). Lysine and Arginine were classified as stronglybasic amino acids, Aspartic Acid and Glutamic Acid as strongly acidicamino acids, Asparagine, Cysteine, Glutamine, Sering, Threonine andTyrosine as other polar amino acids, and Alanine, Isoleucine, Leucine,Phenylalanine, Tryptophan and Valine as hydrophobic amino acids. Tandemrepeat domains of the tandem repeat proteins were analyzed in a sameway. As a control, 108 genes, which were randomly selected from the L.infantum gene database, were also analyzed isometric points and aminoacid compositions of their deduced amino acid sequences.

Example 13 Expression of Recombinant Proteins

Sequences encoding whole or partial tandem repeat domains ofLinJ20.1220, LinJ25.1100, LinJ32.3710 were amplified by PCR. Theamplified PCR products were inserted into multi cloning sites of pET28aand the inserts were confirmed their sequences matching with the ones ondatabase. The vectors with the inserts were transformed into expressionhost E. coli and the recombinant proteins were purified as 6×His-taggedproteins using Ni-NTA agarose (Qiagen Inc., Valencia, Calif.). Theconcentrations of these proteins were measured by BCA protein assay(Pierce Biotechnology Inc., Rockford, Ill.).

Example 14 Recognition of Tandem Repeat Proteins by Sera FromLeishmaniasis Patients

To evaluate antigenicity of the tandem repeat proteins, ELISA wasperformed using 200 ng antigen per well in 96-well plates. Sera fromvisceral Leishmaniasis patients (Sudan), cutaneous leishmaniasispatients (Brazil) and healthy individuals (United States) were used at1:100 dilutions for the ELISA.

The visceral Leishmaniasis patient sera showed significantly strongerreactivity to all the recombinant proteins than sera from non-visceralLeishmaniasis groups, i.e. tuberculosis, malaria and cutaneousleishmaniasis patients or healthy individuals, despite the finding thatcutaneous leishmaniasis patients showed antibody responses to LiSLA(FIG. 6). Among the tested proteins, rLinJ16.1750r2 was the bestantigen, and was recognized strongly by visceral Leishmaniasis patientsera with a high degree of specificity. Next, rLinJ16.1750r2 was testedwith additional Sudanese visceral Leishmaniasis patient sera. Among 35sera tested, 34 showed antibody responses to rLinJ16.1750r2 (the cutoffvalue was the mean+3 SD of healthy controls: FIG. 6). The sensitivityusing rLinJ16.1750r2 was 97%, comparable to that of rK39 (35/35, 100%:FIG. 6). Mean O.D. values to rLinJ16.1750r2 and rK39 were 1.159 and1.771, respectively.

Although these 35 sera were 100% positive using rK39, eight sera showedlow reactivity to rK39 (OD values were <1.0: FIG. 6). These eightsamples were tested for reactivity to rLinJ16.1750r2, rLinJ22.1590r3,rLinJ28.2310 or rLinJ33.2870r1 to examine whether or not those antigenscould complement rK39 for more sensitive antibody detection. Five of theeight sera showed better responses to the new antigens than to rK39 (No.3-7 in FIG. 6). Five patients (No. 3-7) showed better responses torLinJ22.1590r3, four (No. 4-7) to rLinJ28.2310, and three (No. 3, 5 and6) to rLinJ33.2870r1. Finally, rLinJ22.1590r3 was recognized weakly byall the eight sera compared to rK39.

Example 15 ELISA Analysis of Tandem Repeat Proteins Identified bySerological Screening and Bioinformatic Analysis

Recombinant tandem repeat proteins or L. infantum promastigote solublelysate antigen (LiSLA) were diluted in ELISA coating buffer, and 96-wellplates were coated with rK39 (50 ng), other recombinant proteins (200ng) or LiSLA (1 μg) followed by blocking with phosphate-buffered salinecontaining 0.05% Tween-20 and 1% bovine serum albumin. Next, the plateswere incubated with patient sera (n=16) as well as healthy controls(n=8) at 1:100 dilution and then with horseradish peroxidase-conjugatedanti-human IgG (Rockland Immunochemicals, Inc., Gilbertsville, Pa.). Theplates were developed with TMB peroxidase substrate (KPL) and read by amicroplate reader at a 450 nm wavelength (570 nm as a reference).

Compared to healthy controls, higher levels of antibody were detectedbeing bound to tandem repeat proteins not only from serologicalscreening but also solely from the bioinformatic analysis in VL patients(Table IV) (FIG. 6). This demonstrates that tandem repeat proteins notonly from serological screening but also identified solely by thebioinformatic analysis are antigenic.

TABLE IV Reactivity of L. infantum Tandem Repeat proteins in ELISA PSaSize OD: OD: OD: Recombinant (aa) CNa (kDa) VL HC P value Identified byserology rLinJ05.0380r6 38 6 28 0.786 0.142 ** rLinJ16.1750r2 73 2 180.847 0.058 *** rLinJ22.1590r3 28 3 12 0.474 0.042 *** rLinJ28.2310TR105 2.2 35 1.326 0.123 *** rLinJ33.2870r1 148 1 18 0.476 0.137 **rLinJ34.2140r2 83 2 20 0.327 0.126 ** Identified solely frombioinformatics rLinJ11.0070r2 46 2 12 0.359 0.065 *** rLinJ21.2010TR 645.3 38 0.274 0.048 *** rLinJ25.1100TR 22 9.6 27 0.520 0.032 ***rLinJ27.0400r2 68 2 18 0.748 0.117 *** rLinJ29.0110TR 8 28.8 31 0.7240.185 ** rLinJ32.3710TR 33 3.8 17 0.192 0.124 * CRUDE LiSLA 0.885 0.082*** Notes: aPS: length of one copy of the repeat in units of aminoacids, CN: copy number. bMean OD values of VL patients (VL: n = 16) andhealthy controls (HC: n = 8) are shown. P values are from statisticalanalyses using Mann-Whitney test. *P < 0.05, **P < 0.01. ***P < 0.001.

From the foregoing, it will be appreciated that, although specificembodiments of this invention have been described herein for thepurposes of illustration, various modifications may be made withoutdeparting from the spirit and scope of the invention. Accordingly, theinvention is not limited except by the appended claims.

1. A method of screening for antigenic polypeptides for the diagnosis,or treatment of leishmaniasis in a patient, or immunization againstleishmaniasis in a patient or screening for Leishmania in a blood supplycomprising: (a) constructing a polynucleotide screening library; (b)expressing the expression products of (a); (c) screening the expressionproduct of the screening library by contacting the expression productwith a Leishmania specific antibody from a patient or blood supply anddetecting an antigenic polypeptide by detecting binding of theexpression product and an antibody binding site portion of saidLeishmania specific antibody; and (d) analyzing sequences identifiedfrom screening the expression product of the screening library to selectgenes that are tandem repeat genes and thereby selecting antigenicpolypeptides that comprise tandem repeats.
 2. The method of claim 1,further comprising the step of excluding polynucleotides having tandemrepeat motifs that have a consecutive 8 amino acids or less whenanalyzing genes identified from the screening library to select genesthat are tandem repeat genes.
 3. The method of claim 1 wherein thescreening library is constructed from L. Infantum.
 4. A method ofscreening for antigenic polypeptides for the diagnosis, or treatment ofleishmaniasis in a patient, or immunization against leishmaniasis in apatient or screening for Leishmania in a blood supply comprising: (a)selecting one or more polypeptide sequence or polynucleotide sequence;(b) analyzing the selected one or more polypeptide sequence orpolynucleotide sequence and selecting sequences that comprise tandemrepeats; (c) expressing the selected sequences of (b); and (d) screeningan expression product of (c) by exposing the expression product to aLeishmania specific antibody isolated from one or more biological sampleobtained from one or more patient infected by Leishmania and detectingan antigenic polypeptide by detecting binding of the expression productand an antibody binding site portion of said Leishmania specificantibody and thereby selecting antigenic polypeptides.
 5. The method ofclaim 4 wherein the antigenic polypeptides are used for the diagnosis ortreatment of, or detection of or immunization against leishmaniasis. 6.The method of claim 1, claim 2, claim 3, claim 4 or claim 5, furthercomprising the step of screening the selected antigenic polypeptides bycomparing the homology of the sequences of the selected antigenicpolypeptides to the sequences of polypeptides of organisms that arepotentially infected by Leishmania and thereby selecting one or morepolypeptides that are least homologous to polypeptides of organisms thatare potentially infected by Leishmania.
 7. The method of claim 1, claim2, claim 3, claim 4 or claim 5, further comprising the step of screeningthe selected antigenic polypeptides by comparing the homology of thesequences of the selected antigenic polypeptides to the sequences ofpolypeptides of organisms that potentially infect organisms that arepotentially infected by Leishmania and thereby selecting one or morepolypeptides that are least homologous to polypeptides of organisms thatpotentially infect organisms that are potentially infected byLeishmania.
 8. A method of identifying candidate antigenic polypeptidesfor the diagnosis, or treatment of leishmaniasis in a patient, orimmunization against leishmaniasis in a patient or screening forLeishmania in a blood supply, comprising: (a) expressing, in one or aplurality of host cells, expression products of a polynucleotideexpression library which comprises one or a plurality of candidateantigenic polypeptide-encoding polynucleotides at least one of which iscapable of expressing a candidate antigenic polypeptide that comprises atandem repeat, to obtain a host cell population comprising expressionproducts; (b) contacting, under conditions and for a time sufficient forspecific binding of at least one Leishmania specific antibody isolatedfrom a biological sample from a patient or blood supply to at least oneexpression product, (i) the host cell population comprising expressionproducts of (a) with (ii) said antibody that is obtained from a subjector biological source that has been infected with a Leishmania organism,wherein the biological material is selected from blood, serum and urine;(c) detecting at least one host cell that comprises the at least oneexpression product to which the at least one anti-Leishmania antibodyspecifically binds; (d) isolating from the host cell detected in (c) apolynucleotide that encodes the expression product to which the at leastone anti-Leishmania antibody specifically binds to obtain an isolatedpolynucleotide; and (e) analyzing a nucleotide sequence of the isolatedpolynucleotide of (d) for presence or absence of a tandem repeat,wherein the presence of a tandem repeat indicates the isolatedpolynucleotide encodes an antigenic polypeptide, and therefromidentifying the antigenic polypeptide.
 9. The method of claim 8 whereinthe polynucleotide expression library is constructed from nucleic acidsequences obtained from an organism that is selected from an infectiousorganism and a non-infectious organism.
 10. The method of claim 8wherein the polynucleotide expression library is constructed from anorganism that causes leishmaniasis.
 11. The method of claim 10 whereinthe organism that causes leishmaniasis is selected from the groupconsisting of Leishmania infantum, Leishmania donovani, Leishmaniamajor, Leishmania amazonensis, and a bacterial strain that causesleishmaniasis.
 12. The method of claim 8 wherein the polynucleotideexpression library is constructed from a pathogenic or non-pathogenicmicrobial organism that is selected from the group consisting of abacterium, a virus, a protozoan, a fungus, a yeast, a diplomonadid and akinetoplastid.
 13. A method of identifying a candidate antigenicpolypeptide for the diagnosis, or treatment of leishmaniasis in apatient, or immunization against leishmaniasis in a patient or screeningfor Leishmania in a blood supply, comprising: (a) expressing, in one ora plurality of host cells, expression products of a polynucleotideexpression library which comprises one or a plurality of candidateantigenic polypeptide-encoding polynucleotides at least one of which iscapable of expressing a candidate antigenic polypeptide that comprises atandem repeat, to obtain a host cell population comprising expressionproducts; (b) contacting, under conditions and for a time sufficient forspecific binding of at least one Leishmania specific antibody isolatedfrom the biological material to at least one expression product, (i) thehost cell population comprising expression products of (a) with (ii)said at least one antibody that is obtained from a subject or biologicalsource that has been infected with an infectious organism, wherein thebiological material is selected from blood, serum and urine; (c)detecting at least one host cell that comprises the at least oneexpression product to which the at least one anti-Leishmania antibodyspecifically binds; (d) isolating from the host cell detected in (c) apolynucleotide that encodes the expression product to which the at leastone anti-Leishmania antibody specifically binds to obtain an isolatedpolynucleotide; and (e) analyzing a nucleotide sequence of the isolatedpolynucleotide of (d) for presence or absence of a tandem repeat,wherein the presence of a tandem repeat indicates the isolatedpolynucleotide encodes an antigenic polypeptide, and therefromidentifying the antigenic polypeptide.
 14. The method of claim 13wherein the polynucleotide expression library is constructed fromnucleic acid sequences obtained from an organism that is selected froman infectious organism and a non-infectious organism.
 15. The method ofclaim 13 wherein the polynucleotide expression library is constructedfrom an organism that causes leishmaniasis.
 16. The method of claim 15wherein the organism that causes leishmaniasis is selected from thegroup consisting of Leishmania infantum, Leishmania donovani, Leishmaniamajor, Leishmania amazonensis, and a bacterial strain that causesleishmaniasis.
 17. The method of claim 13 wherein the polynucleotideexpression library is constructed from a pathogenic or non-pathogenicmicrobial organism that is selected from the group consisting of abacterium, a virus, a protozoan, a fungus, a yeast, a diplomonadid and akinetoplastid.